TurboTax prepared your tax forms based upon the information you entered into the program. It sounds like the W-2 forms may not have been entered correctly in the program when you prepared your return.
I recommend reviewing all of your W-2 forms and totalling up the amount of the federal income tax withholdings in box 2 and comparing that total to the amounts reported on the IRS notice notifying you of the changes. If the IRS is correct, then you can follow the instructions on their notice.
As far as the $13,000 paid with extension, that would only be entered under Deductions and Credits, and specifically under Payments with 2023 federal extension based upon input in the program.
If you feel the error was the result of something on the TurboTax side, you can submit a request for a review using this link.
Please read through the information and if you qualify for the terms, you can proceed to submit your information which will be reviewed. If the claim is approved, you may be reimbursed for any penalties and interest from the date of your first notice from the taxing agency.
@cytibbs
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