applied payment

If you open the history window for the invoice (press Ctrl-H while the invoice is the active window) is there a payment shown as applied to it?

If nothing is applied, and the invoice's open balance is less than the original amount, then something is corrupted. Rebuilding the file (Rebuild is on the File | Utilities menu) will recalculate the invoice open balances and so should fix it in such a case.

I found the mistake on a completely different payment where a discount was applied twice.  I'm sure that was my fault so I need to slow down and double check the transaction before completing.  Thank you for your response!