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“It’s a huge disappointment,” said Gills boss Justin Edinburgh after seeing his team leave Fleetwood with nothing.
Edinburgh felt his side bossed the second half but watched on as another lapse at the back proved costly.
Edinburgh said: “I thought we dominated possession in a pretty even first half. We spoke at half-time and the response from the players was exactly what we asked.
“They played with a real purpose, good energy and good tempo, which we couldn’t get in the first half. We got it in the second.
“It was leading to the home side playing on the counter attack but yet again, a game we dominated second half, we ended up losing.”
Match report: Fleetwood Town 2 Gillingham 1
There were protests after Fleetwood took the lead midway through the first half as the players thought David Ball was offside when he tapped the ball past Stuart Nelson.
But the Gills boss said: “I don’t believe it was offside. I think when the ball was played he was onside.
“In real game-time it may have looked offside for the players but we have been able to see it again.
“We had to do better in the initial build up to the play, from the clearance we were out of shape but we had opportunities to deal with it, we allowed him to go into the box and once he is in there it is difficult to make contact.”
Jake Hessenthaler levelled the scores in the second half but Fleetwood won it late on. Paul Konchesky was beaten on the left flank and from the resulting cross, Ashley Hunter netted.
Edinburgh said: “We got the goal and it looked like we would go on and win but we have been the undoing of ourselves and we are getting punished.”