The Sulphurites took an early lead against their promotion-chasing hosts when Jack Muldoon notched his 10th goal of the season, but were powerless to stop the home team from turning the game on its head in the second half.
The 78th-minute dismissal of experienced midfielder Kerry while the contest was still in the balance at 1-1 certainly did not help, though the Town chief does not believe that moment can be classed as a game-changer.
"We didn't lose the game because of Lloyd Kerry's sending off, we lost the game because we lost control on the ball earlier on," Weaver reflected.
"I don't think it was a case of being unfortunate. Having had a really strong start and scored a good goal to go into the lead, we didn't really carry it forward. We went into protective mode.
"Perhaps it's understandable to a certain extent because they are right up there, but we didn't take the game to Cambridge, who you have to accept are a well-oiled machine and really good at what they do.
"They changed their system and matched us up and were better at it than we were. The momentum turned and went against us and I think they passed the ball better than we did and caused us problems.
"It did feel as if it [the equaliser] was coming, if I'm honest. We had to change the system three times to try and stem the tide and it was difficult going. The legs became a little bit weary and we were getting picked off."
Of the incident which saw Kerry handed his marching orders for raising his hand to Harry Darling just 13 minutes after arriving as a substitute, Weaver said that he felt that his player left referee Carl Brook with a decision to make despite not making any contact with the opponent's face.
"He was frustrated with a free-kick that had been given against us and a player just rushed up to him and was in his face and Lloyd moved his hand towards his face," he added.
"He didn't slap him or punch him, but he did raise his hand without making contact and the problem is that you are putting the referee in a difficult position.
"Straight away after the game he's regretted it. He had a bit of a red mist moment, it's perhaps frustration at not being in the starting XI having been used to that, but there's no way I'll lambast the lad, he's been absolutely fantastic for this football club and I have sympathy.
"I understand his frustration and that sometimes the edge can be a bit too close and you can go over it if you're a winner and want to do so well."
Thick fog made for tricky playing conditions at the Abbey Stadium on Saturday afternoon, but couldn't prevent visiting Harrogate from taking the lead when debutant Josh March rose well to help Connor Kirby's pass into the path of Muldoon, who calmly beat Dimitar Mitov one-on-one.
March then went close to doubling the away lead with a well-struck left-footed effort which narrowly cleared the cross-bar, though that was about as good as things got for Town as an attacking force.
The second period belonged to the home side, who enjoyed a sustained spell in the ascendancy and eventually levelled matters on 71 minutes after Joe Ironside got across the near post to finish off Wes Hoolahan's inviting low delivery from the left.
Kerry was then given his marching orders, and barely three minutes later Hoolahan decided the game, stroking a cultured finish into the bottom corner of James Belshaw's goal from just outside the box.
Defeat sees Town drop one place to 18th in the League Two standings and leaves them just five points clear of the relegation zone.