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I've got some ways to correct this, samram.
When the customer is overpaid, you'll want to create an expense or check instead of a refund receipt. Then, link expense or check to the payment, so the customer's balance is zeroed out.
Here's a sample screenshot:
I'm adding this article that you can use for reference: Record a customer refund in QuickBooks Online.
You can also run the Transaction List by Customer report to view the transactions.
If you need anything else, please let me know and I'll get back to you as soon as I can. Take care!