Boyd's side were beaten 26-20 at the CBS Arena after conceding an avalanche of penalties after the break.
Saints had gone in at half-time level at 10-10 despite largely dominating the first 40 minutes.
And Wasps made them pay for not capitalising on their first-half territorial advantage as the hosts secured their second win in three Gallagher Premiership games this season.
For Saints, it was a first defeat, and there was no shortage of controversy, with the away side likely to feel aggrieved that Gabriel Oghre only saw yellow for a high tackle on Alex Mitchell.
But in the end, it was Saints who were the ultimate sinners, allowing Jimmy Gopperth to boot a couple of penalties that made sure of the Wasps win.
"There were a lot of factors but the biggest one that's been troubling us for the past two or three weeks came home to roost in the end," Boyd said. "We gave away so many dumb penalties that kept them in the game it was ridiculous.
"That discipline around the ruck area, around the maul area, around the tackle area ultimately killed us.
"The guys that came off the bench were a bit frustrated and if you look at who gave the penalties away it was the guys who came on and wanted to make a difference, despite the fact we talked about that at half-time.
"It was frustrating, we tried to keep the tempo up and they tried to slow it down for long periods of time.
"We thought we might get some reward in the last 20, but it wasn't to be."
James Fish's last-gasp try earned the losing bonus point that means Saints head into their bye weekend with 14 points from four matches.
Boyd's side return to action against Worcester Warriors at cinch Stadium at Franklin's Gardens on October 22.
And the Saints boss said: "We'll see how important that losing bonus point is in 20 weeks' time.
"We know it's about accumulation of points and we're disappointed not to come away with four from here.
"We've got a point and we've got a bye week next week so we'll regroup for Worcester at home.
"There's a lot of work to be done."