Before we sort things out, I'd like to clarify what's the status of the payment an in the customer's Transaction List page, does it show negative in the Total column. This way, we can modify it or we'll apply the overpayment as credit to the customer.
Let me show you how to review the payment to get started.
Go to the Sales menu and select Customers.
Select the customer who had the payment and then click Transaction List.
From the list, look for a Payment that has a Partial status with a negative amount.
Open it and let's see what invoice was paid and the amount received.
If there are no invoices linked to the payment it'll show as unapplied or as an existing credit to your customer. When we try to create and invoice or pay an existing one, a Credits section will show in the Receive Payment page. You can apply it to zero out the customer's balance as well as the credits.