@royper tbh it's unlikely to be a bug, TT is very solid on it's core tax calcs.
Penalty is calculated quarterly and if you had uneven payments then you can get underpayments or overpayments so it depends how those quarterly payments line up with the safe harbor threshold.
If you are on desktop then go to Forms mode, if you don't see Form 2210 in the list of forms then double-click on the penalty line on Form 1040 and double-click again on the penalty line in the 1040 worksheet to bring up Form 2210 which will show you how the penalty is being calculated.
If still stuck if you can provide more specifics then someone here may be able to explain further.
