Retirement tax questions

Client reported incorrect excess Roth contribution of $600 on her 2019 tax return.  She paid the 6% penalty on her 2019 tax return, and now apply that $600 to her 2020 Roth contribution.  The problem is, the excess in 2019 was actually $650.  She paid the 6% penalty on the 600 but not the $50.  She did not withdraw and now apply the whole $650 as 2020 Roth contribution.  How do we remedy the penalty on the $50 that was not paid in 2019.  TTO not letting us force the form 5329 to enter the penalty.  Can we enter the $50 as taxable income for 2020, but still how to report the 6% penalty on the $50 for 2019?