"I thought it was a fantastic performance despite the result," said assistant manager Mark Lillis after the game at Sincil Bank.
"We hit the bar and we created some decent chances, but they defended well to be honest.
"We can't keep giving teams a two-goal start, but it is all a part of learning. We can't fault the lads' effort, and we passed the ball around like we wanted to, sometimes you just need that little bit of luck to go for you, but the way you get that is by staying confident."
Northampton meanwhile will be keen to take a maximum points haul from two home games in the space of five days with first Morecambe and then Aldershot to come to Sixfields.