I'm here to help you sort things out, corina-felber.
So far, we haven't received any similar issues reported. QuickBooks Online offers automation features, such as automatically applying payments to an invoice.
If this feature is turned on and your customer has an available credit, this will automatically link to your open invoice and marking them as paid.
To turn off this feature, here's how:
If you want to unlink the payment, see the steps below to complete the process.
To know more about this feature, check out this article: Create and apply adjustment notes or delayed credits in QuickBooks Online. It contains more details on how to manage adjustment notes as well as applying a delayed credit in QuickBooks Online.
Leave a comment below if there's anything else we can help. I'll be right here to help you with anything about QuickBooks. Have a nice day!