I think you may have accounted for the payment correctly but duplicated the deposit somehow.
It's the invoice and the duplicated deposit that are showing up in your sales account. Double-click on the deposit entry amount to bring the deposit up on your screen. Add a row at the bottom of your deposit charged to your sales account using a negative amount that's exactly the same (except for being negative) as the duplicated amount.
Then save the deposit and don't do that anymore.