The Cobblers found themselves 3-0 down at half-time but substitute Brett Williams pulled a goal back in the 65th minute.
Boothroyd's side then twice hit the woodwork and he felt his men were right out of luck.
He said: "It was a strange game, and we conceded three poor goals but I don't want to make excuses.
"Our performance was not as bad as when we lost at home to Bradford, from my point of view.
"If we had scored another, you never know. It could have gone our way. But when you're down the table things like that don't go for you. I'm sure that with some surgery in the summer we will be okay."
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