That situation shows that you did not record the payment correctly when you received it. You will need to find that transaction and correct or replace it.
The easiest way to record payments is through the Sales Invoices tab. View the sales invoice and click on Receive Money. The specific sales invoice will automatically be selected and the amount in full filled in. You can edit any the information.
You can also do it through Bank Accounts or Cash Accounts tabs. Receive Money in the appropriate account and allocate the payment to Accounts receivable and the appropriate invoice.
The fact that your invoice is still showing as unpaid means the payment went somewhere else. Check Suspense, which should always be empty. One mistake people make in accounting is to allocate payments against sales invoices directly to some income account. That should have been done when the invoice was created, not when payment is received. The receipt goes to clear the account receivable.