After you file

Respond to them proving that they were wrong ... first start with a simple phone call to the number on the notice ... simply say "I don't understand how I could owe when I already paid ?   Please explain it to me. "  Be prepared to support the payment ... have a copy of the cancelled check or bank/CC statement showing the payment in hand.

https://www.irs.gov/individuals/understanding-your-cp60-notice