Welcome aboard to the Community. I'm here to provide help with any questions you may have regarding customer payments.
Let me start by asking a few questions about your concern. Did the customer want a refund or a credit to the next invoice? Were you able to verify the payment?
You can go to the Merchant Service Center to determine if your customers overpaid the invoices. I'm adding the detailed steps on how you can access this screen within QuickBooks Online:
You can also let your customer review their bank statement to determine if it's charged twice. If you're unable to locate any duplicates, please give us a call.
Our Phone Support Specialists from QuickBooks Payments will need to check the payment and perform the necessary action.
Once you've verified the overpayment and the customer wants a refund, I'm adding the article I recommend on this:
Refund customers for overpayments.
Any additional information you can provide will help to ensure a timely solution. I'll be on a look out for your response.