Gillingham boss Peter Taylor was furious Colchester's first goal was allowed to stand in their 3-0 defeat.
Former Crystal Palace and Birmingham forward Clinton Morrison sealed the points for the U's three minutes from time after Sanchez Watt had ended his goal-drought soon after half-time - his first goal since October 2012.
There was still time for substitute Freddie Sears to add a third in the dying moments, but Taylor insisted Watt's effort should have been chalked out.
Taylor, who felt the Gills were a shadow of the side that beat Wolves last time out, said: "That was not good enough.
"I think the first half was very even, we had chances to score and so did they.
"I think had we have broken away with a bit more quality in the first half, there was a goal there. Unfortunately we didn't carry it on.
"We're extremely unhappy with the first goal. We believe it was offside.
"The fella (Marcus Bean) was interfering (when Sanchez Watt shot), but apparently the linesman said because he let it through his legs, it's ok.
"That changed things, and Colchester deserved to win the match on the basis of their second-half performance.
"The first goal shouldn't have made as much difference as it did. Our heads dropped, and we didn't play anywhere near the way we have recently. They played through us too easily after that.
"Last Friday against Wolves I could have named quite a few players for the man of the match, but there weren't many plusses in our performance. We were not right and that's not acceptable."
It could have been more for Colchester, but Gills goalkeeper Stuart Nelson denied Luke Garbutt on several occasions, while Brian Wilson saw his effort cleared off the goal-line by Leon Legge
Cody McDonald had Gillingham's best chance in the first half with a 20-yard effort that went narrowly wide, while Danny Kedwell headed over the crossbar from Jake Hessenthaler's corner.