maybe timing issue as underpayment is assessed quarterly not just total annual amount - if the refund was applied to your estimated taxes after the Q1 estimated tax deadline (4/15) you may still be assessed an underpayment penalty for Q1 even tho you met the annual 'safe harbor' requirement in total.
In desktop version you can click in Forms mode thru the penalty line on Form 1040 or go to Form 2210 directly and see the calculations and which quarter got the penalty and why, not sure equivalent process in TT online but you be able to see Form 2210.
Adopting the Annualized Income method may not help the penalty if the issue was the timing of the payment, rather than the timing of your income/tax and that was otherwise uniform thru the year.
