What usually causes this is QuickBooks auto-apply credits or auto-matching from the bank feed, so payments end up stuck on the wrong invoices. The quick fix is to open the customer, edit each payment, and re-check the right invoice, then save. If it’s part of a bank deposit, open the deposit and fix the lines there. To stop it from happening again, turn off Automatically apply credits in Account and Settings - Advanced - Automation, and make sure your bank rules aren’t auto-adding transactions straight to A/R. For invoice messages, set a default under Sales - Messages so you don’t have to edit each one manually. It’s annoying, but once you clean up the payments and switch off those auto settings, the problem usually stops repeating.
