If you owed a penalty then the program would have asked you about the prior year information in the 2210 section and it would have applied the correct exemption automatically. Sounds like you did not supply the proper 2019 information required for the form 2210 to be calculated properly. Sadly if you've already paid the balance due all you can do is send in a form 2210 with an amended return to get the IRS to refund you the excess penalty paid.
