- There are a lot of non-obvious Shopify store problems that can sneak under the owner's radar.Â
- Theme updates preserve your editor settings but wipe any code edits made to the theme's core Liquid, CSS, or JavaScript. So, make your customizations in separate non-theme-native files.
- Express checkout buttons like Shop Pay and Apple Pay jump straight to checkout, so cart upsells, warnings, and validation never run for those buyers.
- Forms can get tricky: the customer might see a success message even when the submission goes to spam or nowhere at all.
- A monthly 30-minute QA check catches nearly all 15 of these before customers do.
Here are the most common Shopify store problems I see time and time again: mobile layout breaks, theme updates overwriting custom code, variant logic failures, 404s after URL changes, and forms that fail.
What happens is that the store looks fine (perhaps even awesome) to the owner...buuuut, broken to the customer.Â
For each of these Shopify store whoopsie-daisies I'll cover what it looks like, why it happens, and how to catch it.
Shopify designers/developers, this doubles as a handoff QA list. Founders, run through this so you can banish that nagging feeling that something's off.
If you're still in setup mode, start with these common Shopify mistakes first, then come back here.
What are the most common Shopify store problems?
- Broken mobile layouts
- Theme updates that wipe out your customizations
- Shipping options that disappear at checkout
- 404s after URL and handle changes
- Contact form submissions getting lost
- Slow or broken images
- Discount codes that stack when they shouldn't
- Express checkout buttons that skip your cart logic
- Custom fonts that don't show on mobile
- Animations that crap out on Safari and iOS
- A favicon that's still the default
- Missing SEO metadata
- Placeholder links and dead-end buttons
- Color contrast that fails accessibility standards
- Layouts buckling under the weight of real client edits
1. Broken mobile layouts
So. In general, Shopify themes come quite well mobile-optimized out of the box (yay!). But this can easily go out the window the second you add any customizations or apps (boo!).
Well over half of eCom traffic is mobile, yet nearly every store gets designed, reviewed, and approved primarily on a desktop monitor, (because the theme editor defaults to desktop preview and it's just human nature to want to look at the "full" version of the site).Â
The common "oops I messed up the mobile layout" culprits: fixed pixel widths, 100vw values (which ignore the scrollbar and cause horizontal overflow), and custom sections that never define behavior below the theme's breakpoints.
Dawn switches layouts at 749px and 989px, so a section with no rules below those points is kinda YOLO-ing it on phones.
This free Chrome extension is going to be your best friend for easily testing mobile layouts on desktop.Â
But, still be sure to do a final check on a real-life phone because iOS Safari has some special quirks that can cause things to go haywire.Â
Scroll through every page on the phone and watch for sideways movement, too big or chopped-off text, and things overlapping when they shouldn't.Â
2. Theme updates that wipe out your customizations
One of the most eye roll-inducing things on Shopify is going through the process of updating a theme if/when you've got lots of customizations that are going to be yeeted out of there the minute you hit "Update".Â
The good news is that your theme editor customizations (colors, sections, settings) live in JSON files and generally survive an update.
Code edits to the theme's core Liquid, CSS, or JavaScript files often do not, because updating installs a fresh copy of the theme's code.
Keep custom code in self-contained snippets and sections instead of editing core theme files (ex. adding a theme-custom.css stylesheet instead of editing base.css).Â
3. Shipping options that disappear at checkout
Nothing kills a sale quite like a customer making it all the way to checkout and getting hit with “Shipping not available for this address.”
This can happen when you add new products, change shipping profiles, start selling to a new country, adjust free-shipping thresholds, or have inventory sitting at a location that isn’t set up to fulfill that particular order.
Any time you make changes to products, shipping, or the countries you sell to, run a couple of test checkouts yourself.
Try your most common destinations, a higher-value cart, a lower-value cart, and any products with their own special shipping rules.Â
4. 404s after URL and handle changes
Shopify handles redirects pretty elegantly. When you edit a product handle a "Create a URL redirect" checkbox appears, ticked by default.
The 404s typically come from the edge cases: someone unticks that box, a bulk CSV handle edit creates no redirects at all, a deleted product leaves nothing behind, or links added as raw URLs keep pointing at the old handle until you change them out.
The problem here is that old URLs might be sitting in a Google result, an old email, or an influencer's caption.Â
Head over to Online Store > Navigation > View URL redirects to fix this. Here, you can add redirects one at a time or import them by CSV in bulk, one of things you can ask Claude to do on your Shopify store).Â
To help detect where your site is spitting out 404s, the Pages report in Google Search Console lists every "Not found (404)" Google has hit.Â
This is something you'll want to keep a close eye on when restructuring things in your store, like when you're setting up Shopify collections and handles get renamed in bulk.
5. Contact form submissions getting lost
Forms submissions are a sneaky one. Shopify’s native contact form sends submissions to the Sender email listed under Settings > Notifications, so an outdated address, broken forwarding setup, or inbox rule can lead to customer messages getting lost in limbo while they still receive a perfectly reassuring success message.
Email authentication is worth checking too. Gmail and Yahoo tightened their sender requirements in 2024, and Shopify now expects branded sending domains to be authenticated with SPF/DKIM and DMARC. If yours isn’t, Shopify may rewrite outgoing emails to a shopifyemail.com address to keep them deliverable (which is usually your clue that the email setup needs attention).
Once a month, submit a real test through every form on your store and confirm it arrives (check spam too if it doesn't).
6. Slow or broken images
Shopify low key does a lot of the heavy lifting when it comes to image optimization: it auto-converts your images to WebP or AVIF and generates responsive sizes for different screens. This is great for improving your site loading speed.Â
The catch is that this auto-optimization only happens if it's properly written into your theme. If the theme (or your custom sections) mishandle the code behind the images, this causes cause layout jank (Cumulative Layout Shift in Google terms)—AND a raw 4MB upload bypasses responsive sizing and bogs your site down.
How to check this by page: open Chrome's DevTools, go to the Network tab, filter to Img (you may need to refresh), and sort by size. The offenders float straight to the top.Â
7. Discount codes that stack when they shouldn't
Every Shopify discount has a "Combines with" setting that either allows or disallows it to combine with other categories of discounts (product, order, and shipping).
It can be easy to just say "yep let's turn all those combos on", but if you're not careful, suddenly you might find a handful of automatic and code and shipping discounts combining together. This can result in a "they paid WHAT for that order?!" type of situation if you're not careful.Â
Audit the Combinations panel on every active discount, then run test checkouts pairing each automatic discount with each live code. Also be sure to keep an eye on your Sales by discount report for numbers that look a little too generous.
If revenue feels lower than your traffic deserves, discounts are one of several suspects; my breakdown of traffic but no sales covers the rest.
8. Express checkout buttons that skip your cart logic
Dynamic checkout buttons (Buy It Now, Shop Pay, Apple Pay, Google Pay) are great because they can streamline things for your visitors, but they come with a big caveat: they jump straight from the product page to checkout.
This means that buyers using express checkout buttons miss things like upsells, minimum-order warnings, and gift options that are a part of your cart.
If your cart bells and whistles are nice-to-have, leave the express buttons enabled and accept that some buyers will skip the cart.
If the extras in your cart are load-bearing (for example a required customization), disable dynamic checkout buttons in your theme settings or move these further up the customer journey than the cart.
9. Custom fonts that don't show on mobile
Shopify’s built-in fonts are usually pretty reliable, so this one mostly applies if you’ve uploaded your own brand fonts or connected something like Adobe Fonts.
Custom fonts can randomly stop showing if they were added incorrectly, tied to an old theme, hosted somewhere that’s no longer available, or connected through an account or subscription that expired.
And, sometimes everything looks perfect on your laptop (where the custom font is installed on your machine) while mobile visitors are seeing a completely different font.
This is another reason why it's a good idea to make it part of your testing checklist to check your site on a real phone.
Pay attention to headings, buttons, menus, and anywhere the brand font is especially obvious.Â
Psssst - I have a free tool that lets you add your custom brand fonts to your Shopify store without writing code OR an app (seriously groundbreaking). Â
10. Animations that crap out on Safari and iOS
Safari's engine is kind of a PITA when it comes to a lot of things web design. The cherry on top is that iOS makes every browser on an iPhone use it.Â
A common Safari/iPhone browser gotcha is that an animation that's silky in Chrome Desktop can stutter on the phone in your customer's hand (yes, even if they're using Chrome mobile—because it's still forced to use Safari's engine under the hood).
If something looks glitchy on your iPhone, your best bet is to simplify or disable that animation on mobile (and if you didn’t build the site yourself, send your developer a screen recording so they can reproduce it).
11. A favicon that's still the default
If you never uploaded a favicon, your store shows a generic globe or a blank square in every browser tab (🥲). Google also displays favicons in mobile search results, so the default haunts you into the SERP where shoppers are comparing you against brands who bothered.
Upload one at Theme settings > Logo, then look at your browser tab and marvel at how much better that feels.Â
12. Missing SEO metadata
Shopify auto-fills page titles and descriptions from your content, which is kind of nice but also way less strategic than you probably want to be.Â
This metadata lives in two places.
- Your homepage title and description live in Online Store > Preferences.
- Every page, product, and collection has its own editable "Search engine listing" panel at the bottom of each item's admin.
Stores hanging out on Google with "Welcome to our store"-type titles don't breed trust or credibility with their visitors, so make sure that all of your store's metadata is looking buttoned up.Â
13. Placeholder links and dead-end buttons
It happens to the best of us: when building a site, that page isn't ready yet, so we pop a "#" in the button as a placeholder and call it a day.
In the same vein: leaving social icon links heading nowhere, or the theme developer's social accounts that populate them until you change them out.Â
Manually click every. button. on. your. store. (Or, have Claude Code do a sweep for you).Â
14. Color contrast that fails accessibility standards
WCAG 2.1 AA demands a 4.5:1 contrast ratio on normal text and 3:1 on large text (24px and up, or around 18.7px bold).
Shopify theme color schemes will happily let you go willy-nilly with brand colors that are nowhere near this. Two things to also beware of:
- All of those super cute Pinterest color schemes—the vast majority of them have "orphan colors", which don't pair with any other color in the palette accessibly.
- Claude has a baaad habit for spitting out totally non-accessible color combinations when it's designing something for web
This one is a double whammy: customers can't easily or comfortably read what's on your site, and you're exposing yourself on the accessibility front.Â
Run all your potential color combinations through my free palette checker tool so you can rest easy knowing they meet this important standard.
15. Layouts buckling under the weight of real client edits
The store looks smokin' hot at handoff...then your client writes a 3-line headline and things start to look look very questionable. The client did everything right, but the section was only ever built for one specific set of content.
A sturdy Shopify section layout should ideally be able to handle longer headlines, missing images, different image shapes, and varying numbers of blocks.Â
Before handoff, test every section with the messiest realistic content you can think of: the longest headline, no image, the maximum number of blocks—and then all of those at once.Â
Frequently Asked Questions
Usually because something in your theme isn’t adapting properly—it could be an oversized image, long line of text, app widget, pop-up, or a custom section that looked fine on desktop but wasn’t tested enough on mobile.
Check your homepage, product pages, cart, menus, and pop-ups on an actual phone (especially an iPhone). Look for text getting cut off, buttons overlapping, images spilling off the screen, or the page sliding sideways when you scroll. If you spot any of those, it’s usually a theme or app styling issue that needs a small mobile-specific fix.
Usually, the changes you made through Shopify’s visual theme editor—things like colors, fonts, sections, images, and page layouts—carry over when you update your theme.
Custom code is where you need to be a little more careful. Shopify can carry code edits into the new version when they don’t conflict with the update, but some edits may need to be added back manually.Â
Your old version stays in your theme library, so you’ve still got a backup to reference if anything looks off after the update.
Usually, yes. When you change a product’s URL inside Shopify, you’ll get an option to automatically send anyone visiting the old URL to the new one. Keep that box checked and Shopify will handle the redirect for you.
Where people get into trouble is after bigger catalog changes, migrations, bulk edits, or deleting products. It’s worth checking your redirects under Content > Menus > View URL Redirects, especially after a big product cleanup.Â
Shopify sends contact form submissions to the Sender email listed under Settings > Notifications. If you’re not seeing them, double-check that address first, then check your spam folder and any forwarding or inbox rules that might be catching them. Send yourself a test message through the form and make sure it arrives. If it doesn’t, you’ve got an email delivery issue that you should get fixing before a real customer’s message disappears into the void.
Buttons like Buy It Now, Shop Pay, and Apple Pay are designed to get customers to checkout as quickly as possible, so they can skip your cart completely. This can be a problem if your cart contains important things like upsells, gift options, minimum-order messages, or other steps customers need to see before checking out. If those cart features are important to how your store works, it may be better to turn off dynamic checkout buttons so every customer goes through the cart first.
Do a thorough manual sweep of your store: click through your header, footer, homepage buttons, collection links, and your most important product pages (or, have Claude do this for you and report back). Pay extra attention after deleting products, changing URLs, updating navigation, or launching a new theme. If you find an old URL that should still lead somewhere useful, add a redirect in Shopify.
A quick check once a month is a good rhythm—plus another sweep any time you update your theme, install a new app, or make a bunch of product changes.
It doesn't need to be a huge production. Spend 20–30 minutes checking the store on your phone, placing a test order, submitting your contact form, trying your discount codes, and clicking through the main customer journey.
This kind of regular maintenance catches a surprising amount before your customers do (and it’s a big part of building a six-figure Shopify store).
If you're a founder and this list gave you a knot in your stomach, this is literally what I do all day. A broken form or a stacking discount is usually a same-week fix;Â send me an inquiry and tell me what's misbehaving.
