Cobblers boss Jimmy Floyd Hasselbaink bemoaned both his side's inability score when in the ascendancy and also their lacklustre second-half performance after Saturday's 3-0 home defeat against Scunthorpe.
Northampton had been the better team in a goalless first-half but, having spurned two good chances, they fell to pieces after half-time and paid the price.
Cameron Burgess poked Scunthorpe ahead on 56 minutes before Duane Holmes scored two goals in similar fashion, beating Town's offside trap before coolly finishing, to ease United to victory.
"It was a game of two halves," said Hasselbaink afterwards. "We didn't start the game well for the first 10 minutes but then after that we came into it and I think we were the better side until half-time.
"We created two or three good chances and they also had one good chance but when you're on top and you're in our position in the table, you need to score a goal to relieve some pressure and we didn't do that.
"How we started the second-half was very disappointing. You want to continue on the from the first but we didn't do that and we gave the game away in the first 20 minutes of the second-half.
"The gaps were too far apart. What made us good was that we were very close to them and we put them under pressure and from there we could play.
"But we didn't do that in the beginning of the game and also in the second-half for 20 minutes and I don't know why that was the case.
"We are very good at people under pressure. It doesn't cost a lot more and it's actually harder to sit off and run back 80 yards.
"In that respect, it was disappointing and so was the way we conceded the goals."
The victory was Scunthorpe's fourth league win in a row and eighth game unbeaten in all competitions, but Hasselbaink felt it was a case of his side throwing it away rather than the visitors winning it through their own good play.
"We lost the game instead of Scunthorpe winning it," he added.
"I think they are a very, very good team and they deserved to win and in spells they were difficult to handle but every time they gave us trouble, it was from our mistakes.
"You can't make that many mistakes, especially when you play against a very good team."
On the debatable free-kick which led to the first goal, the Town manager continued: "The first goal was not right, it was not a free-kick.
"But the referee gave it and you still have to defend it and we didn't.
"The second phase is the most dangerous phase but we didn't do it so you forget about the decision of the referee."
John-Joe O'Toole left the ground on crutches and wearing a protective boot after his first-half withdrawal but Hasselbaink was unsure as to the severity of his injury, with his ankle thought to be heavily swollen.