TT incorrectly owe a penalty for excess contribution to traditional IRA, but this was due to a previous year's contribution. How do I correct this?

In order to correct this, don't enter the 2023 late contribution on your 2024 tax return as a contribution. For the 2023 tax return, you should have prepared a Form 8606 - check your tax return to verify you did.  If not, you can do so now.  There may be a $50 late fee assessed unless you have cause.  See: About Form 8606, Nondeductible IRAs to get a pdf form and fill it out, if needed.

Next, since the conversion for both years happened in 2024, it is correct that they were both reported to you on the 2024 1099-R.  In order to ensure no tax is computed on the conversion, since you did not deduct them in the first place, after you enter the 1099-R, continue through the interview until you are asked f you moved the money through a rollover or conversion. Answer that you converted (all of it) to a Roth IRA.