I was prompted to pay my penalty during filing and I said yes, but my 1040 doesn't show this. Where can I find proof that I already made my penalty payment?

[Bsch4477]

The penalty would be on line 38 of your 104. 

[VolvoGirl]

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?