If you do not real owe the customer money then you may have simply applied the customer payment incorrectly. Maybe the payment was assigned to the customer and not to the invoice or maybe the payment was assigned to the wrong customer.  If the payment was assigned to the wrong customer then the wrong customer will have an over payment resulting in a credit balance.

There could have also been a duplicate data entry.  Maybe you forgot you already accepted the payment against the invoice and then did it again.

The other thing that could have happened is that the payment was not entered as a payment to the invoice but simply as a deposit which skips a step.

If this is a recent occurrence it should be pretty easy to find by backtracking against your most recent deposits (customer payments).