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Justin Edinburgh felt his side should have left Oxford with at least a point.
The Gills went close to scoring on several occasions but couldn’t get past a stubborn defence.
Boss Edinburgh said: “I thought we deserved something out of the game.
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Match Report: Oxford United 1 Gillingham 0
“We will always be disappointed about the goal we gave away, because you always feel you can do better.
"In what was our third successive away game I thought we had done more than enough to get something out of the game.
“We hit the crossbar and had one off the line and I feel two penalties should have been awarded first half and a more blatant one in the second half but I am talking about something I shouldn’t be.
“Second half I thought Oxford defended well and made it difficult. Perhaps we just didn’t make that right pass, we were a little anxious to try and switch the play too soon.”
Oxford led into the break and the one goal proved to be enough.
Edinburgh said: “We could have done better. We just had a lapse in concentration and a man ran off us, he dispatched it well.
"They will look at it as a good goal and we will always look at goals conceded and think we can do better, which we could.
“I don’t think you could fault the players. I am not going to criticise. People can think and say what they like.
“Oxford don’t lose many games at their place and we pushed them hard and we deserved something.”
Edinburgh tried to change the game second half, with the introduction of Frank Nouble, but Oxford refused to buckle.
He said: “We put Frank out wide and we put Bradley in the hole, we changed things to try and get Dacky in a central area to get him on the ball.
“But when they are defending a lead they can condense space and they did that, they had two banks of four and maybe one more dropping in. It was difficult. I just felt maybe we rushed that final pass.”