Aidy Boothroyd said he could not fault the effort of his Cobblers players and that they paid the price for a five-minute lapse of concentration at Oxford.
Town went down 2-0 at the Kassam Stadium, with both of the home side’s goals coming in the final minutes of an even first half.
The second was a highly-controversial Danny Rose penalty after striker James Constable - who scored the first - had gone to ground in the penalty area.
Goalkeeping coach Tim Flowers was sent to the stands for protesting that decision and the club could face further disciplinary action if referee Darren Deadman suggests such a course of action in his report.
For Boothroyd, it was another defeat for his side, who remain second bottom in Sky Bet League Two as a result.
“Five minutes of madness cost us,” he said. “We’ve had a good week and we’d created a couple of chances in this game before the bad five minutes.
“I don’t think it was a penalty but they shouldn’t get in there in the first place and that’s our responsibility.
“We huffed and puffed in the second half but we couldn’t do anything really because the game was lost in those five minutes.
“The effort is there, the willingness is there and unfortunately the concentration for that period of five minutes wasn’t there.”