I'm filing an amended return for a withdrawal of an excess IRA contribution. Why am I being charged additional tax when I withdrew the money before the 2019 tax deadline?

I filed my 2019 taxes in march of 2020.  When doing the taxes I realized that I no longer qualified for a Roth IRA contribution.  I had already made the contribution in January of 2019.  I contacted my plan administrator and they withdrew the $6,000 contribution plus the excess earnings on that money and deposited it in my bank account on April 3rd of 2020.  They stated I would get a 1099-R for the excess contribution in January of 2021 and to file an amended return for 2019.

I am working in TurboTax to file my amended return return for 2019.  It has correctly calculated the tax I need to pay for the excess earnings.  However, TurboTax has also applied a 6% additional tax on the $6000 contribution that I made.  Shouldn't I not need to pay the additional tax because the excess contribution and additional earning were removed before the 2019 tax deadline?  If so, how can I remove the additional tax and file the amended tax return?