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?

I contributed $7K for 2024 and $6.5K as a late contribution for 2023 (in April 2024). TT says I owe a 6% penalty each year this money remains in the IRA. I already converted all of my money in the traditional IRA to Roth IRA. How do I correct this and ensure I don't owe a penalty?