Hello and welcome to the Community, user74434
To correct, simply delete the VAT payment by following the steps below:
1. Go to Taxes and select the Payments tab.
2. Select Delete from the Action column. Then select Yes to confirm.
Note: After you delete a payment, the page doesn't refresh automatically.
Leave and come back to the Taxes menu. The payment shouldn't appear anymore, and you can record the payment against the return again.