That's not impossible or unusual, since the IRS penalty runs until they process your return and record the receipt of any payment you made with your return, and the program cannot know that date.
Also, he program calculated the penalty based on when you say you made your estimated payments and how much, and the IRS goes by their own records of what you paid and when. If you believe the IRS has recorded your estimated payments correctly, go ahead and pay the amount you are being billed by the IRS. Our guarantee does not cover an increase in this penalty.