Which penalty? There's an underpayment penalty on 1040 line 38. That is already included in the tax due on line 37 or reduced a refund on line 35a.
Or did you get a 1099R? There is a 10% Early Withdrawal Penalty if you are under 59 1/2. The 10% Early Withdrawal Penalty is automatically included in your tax return and tax due (or reduces your refund). It will break out and show the 10% penalty separately on your return (schedule 2 line 6 which goes to 1040 line 23). Then you get credit for all the withholding taken out on 1040 line 25b.
Or how did it prompt you to pay a penalty? Any penalties in Turbo Tax are included in your tax return. You don't pay them separately. Or did the IRS send you a letter for it?
