Easy fix ... in the file tab step 2 ... if the IRS has already been paid then choose the Mail in a check option then simply don't mail in the duplicate payment .
FYI ... if you entered the CC debit info in the TT system and the IRS rejects the return the CC payment info was never sent to the IRS so the payment was never made so check your CC ... is there an actual charge or just a temp charge that will drop off in a couple of days? If you need to make a payment after filing then make it online at www.IRS.gov/pay
