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Justin Edinburgh blamed referee Nigel Miller for giving Doncaster a route back into Saturday’s game.
The Gills boss was seething at the final whistle after Mr Miller awarded Doncaster a 75th-minute free-kick which the hosts scored from.
Doncaster were trailing 2-0 before Cameron Stewart planted the set-piece past Stuart Nelson and soon after they levelled for a share of the points.
Edinburgh, risking a Football Association reprimand, said: “Again we are talking about the person in the middle who refereed the game, who allowed Doncaster back in the game.
“It was never a free-kick which they scored from and it gave them a lift. They are then back in the game only from a poor decision he has made.
“We were in control, we were absolutely superb. Yes, you can look at us and say we lost a 2-0 lead but there were decisions from last week (at Wigan) and again in this game that have cost us.
“It is disappointing because it was so close to being a complete away performance. We are suffering for poor decisions right now.
“The whole team were outstanding. Stuart Nelson didn’t have a save to make for almost 60 minutes but unfortunately the referee wants to take part in the game and gave them a free-kick which never was, which they scored from and it lifts them.”
Wigan came back from 2-0 down to win 3-2 last Thursday and Edinburgh felt decisions in that game had also proved costly.
He said: “I have had the feedback from the assessor and the first goal at Wigan should have been disallowed.
“We should have had a free-kick for the foul on Donnelly leading up to the corner.
“Again the referee has played a part in them coming back into the game, it’s as simple as that.
“Okay, that only makes it 2-1, but that is something they got not through their good play, it was a refereeing decision and it hurt us badly.”