Payment not applied to sales invoice

After upgrading manager last month I have 2 customers that have appeared with an invoice that is marked overdue and a payment marked overpaid. They both have a zero balance and I cannot figure out why the invoice and payment reappeared and how to apply the payment to the specific invoice and make them go away. Any thoughts?

Your old version must have ben quite old. What you see is the result of changes 2 years ago to how overpayments are allocated. There is a Guide addressing this issue: