The 6% penalty for the excess contribution is calculated on a 2018 Form 5329. You can cause TurboTax to do this by amending your 2018 tax return using 2018 TurboTax. You'll pay that separately from the penalty due with your 2019 tax return.
You'll also have the same penalty on your 2019 Form 5329 as part of your 2019 tax return because the excess remained at the end of 2019.
