Retirement tax questions

The same thing happened to me - I got a notice from NY State that my IRC125 contributions from 2019 (I'm on NY State payroll) were not entered into my NYS taxable income. Fortunately the amount due (penalties and tax owed) is manageable, but I don't understand how this continues to be a persistent problem with Turbo Tax! This is not the first time that this has happened to me.