I have paid what Turbotax estimated i owed before filing for extensionm, and I don't appear to owe anything on Turbotax, but it says I have an underpayment penalty.

Turbotax says i have a $41 late payment penalty. I filed for an extension and paid everything Turbotax said i owed at the time. When requested a penalty exemption, I am back to owing nothing. Is this a bug? How could i owe nothing other than the "late payment" penalty?