Extension details were not correct. Why didn't the program catch that.

Just got a letter from NY saying that I underpaid 30.00 in taxes.  I reviewed my return and saw that I hadn't selected the YES for the extension box.  So, I had extended, sending along the money that I thought I owed.  Then when I filed my federal and non-resident NY income taxes, TurboTax let me get away with not marking the extension box.  The weird thing is, I  updated and said yes and entered the 270 payment I had made, and I owed money!  I went from 0.00 owed to 39.00 AFTER I entered the additional money.  Why did the program let me get away with not saying yes to the extension, considering I filed in October.  Why wasn't that part of my return challenged by the program?