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Justin Edinburgh pointed to Gillingham’s lack of composure as they slipped to a first defeat of the season.
The Gills were caught up in a wide open first half and were unable to recover from going 2-1 down.
“We were possibly a bit too open,” said the Gills manager.
“We didn’t control the game as we have been doing away from home.
“Their goal came against the run of play after we had started well. We had controlled it but we never got back to that, even when we got level.
“I don’t think we were as composed as we should have been.”
Colchester went ahead after just four minutes but Luke Norris levelled shortly after.
Edinburgh said: “We got caught up in a game that was too open and it was disappointing. I thought we were a bit erratic in our decision making.
"The players went right to the end and I probably thought we could have snatched a draw but it wasn’t to be. In terms of effort and application, good, decision making and controlling the game, not so good."
Trailing 2-1, the Gills had the chance to level from the penalty spot but Cody McDonald saw his effort saved.
The manager said: “We have had some good chances, we missed a penalty and had we come away with a draw we would have continued our run.
“Cody has taken every penalty since I have been here. He missed it but his record speaks for itself. We have had other chances but we just have to take the defeat on the chin.”