The Cobblers made it 10 straight wins at Sixfields but left it late as Roy O'Donovan grabbed his third goal of the season five minutes from the end to extend their impressive home run.
Knill said: "This was always going to be a difficult place to come, given the league positions of the two clubs, so it was very disappointing to lose so late on.
"We weathered the early storm and then it was a pretty even game. In the second half we were growing into the game and deserved to get something out of it.
"To concede so late in the game was disappointing but even after that we had a couple of chances to equalise and we haven't taken them. But there were some positives to take out of the game."
Knill was also frustrated with the performance of the officials, adding: "The referee made some strange decisions all game and I don't know how that isn't a penalty when Elliot Benyon was tripped.
"To be fair it was the same for both sides and the officials didn't seem to see what the coaches and players were seeing."