Been doing Shopify app dev for a while now, and the same three issues come up constantly on client projects — sharing in case it saves someone a debugging session:

1. Webhook race conditions on order creation. If your app listens to orders/create and also queries the Admin API for line items immediately after, you'll occasionally get incomplete data because the order isn't fully committed yet. Fix: listen to orders/paid instead, or add a short retry/backoff before your first read.

2. Theme app extensions breaking after Online Store 2.0 migrations. Apps built pre-2.0 that inject via theme.liquid snippets often silently stop rendering after a merchant switches themes. If a client says "the app just disappeared," check whether the block is still registered in the new theme's sections — it usually isn't.

3. Rate-limit death spirals on bulk syncs. Apps that loop through products/variants one REST call at a time hit 429s constantly at scale. Switching to the Bulk Operations API (GraphQL) instead of REST loops fixes 90% of "our sync is slow/broken" tickets.

If you're an agency or dev shop and one of these (or something else entirely) is currently on fire in a client's Shopify app, I do flat-rate fixes — no hourly billing, 48-hour turnaround. Happy to just answer questions here too if you're stuck.