"We've missed a good chance to move up the table," he lamented after seeing the Cobbers pick up three vital points at Sixfields.
"We talked beforehand about feeling our way into the game, but two weak challenges on Kevin Thornton put us behind.
"Confidence was already low following our recent results and once we went behind we had a mountain to climb. We worked our way back into the game, but for the amount of possession we had we didn't work their keeper enough."
League Two newcomers Stevenage are next for Northampton with the two sides meeting at Broadhall Way on Saturday.