UPDATE:
So yesterday I followed your advice and adjusted the number on each 1099-R to reflect what I had withdrawn from each account to meet my RMD requirements. The app continued to show a penalty.
This morning I had planned to delete each 1099-R individually to see what was triggering the penalty. Ended up I did not need to do this? I logged into TT, it opened my tax return, and found that everything was correct. The penalty was gone and the data aligned with my estimates. Not sure why this occurred, but right now the app is processing my return without the penalty.
