Retirement tax questions

My HSA was over-contributed by accident in 2019 and I paid income tax on the over-contributed amount.  However, I did not realize I would continue a penalty until the excess was withdrawn.  Withdrawal done in 2021.  Form 8889-T will not fill out properly to calculate just the 20% penalty so a TTax rep said to override the calculations on form 8889-T, pay income tax again on the amount of the over-contribution and then the calculation of the 20% penalty shows on the 8889-T form.  I'm not happy to pay tax on an amount I already paid but it's not a lot.  However, TurboTax (Desktop) now says I can't e-file because  of the override on the form??  Can this be fixed??