TT implements safe harbor / penalty calcs. But it depends how you met the safe harbor it was thru uneven estimated taxes and you made estimated tax payments later in the year (common for Roth conversions in Q4 for example), you can meet the safe harbor - you could even have a refund - but you may still have underpaid for the earlier quarters. If your estimate tax was late in the year to line up with uneven income earned late in the year then Form 2210 AI may reduce or eliminate it. If your estimated tax was simply late against income earned earlier or throughout the year then AI method won't help.
You can bring up for Form 2210 to see the calculation and why there was an underpayment. If you are on desktop double click thru line 38 to the worksheet and again, it will bring up Form 2210 which may not be shown by default unless you select one of the exception options under Other Tax Situations.
