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Peter Taylor questioned the referee’s time keeping after losing Saturday’s game.
Six minutes of added-on time were indicated by fourth official Danny Gratton but referee Kevin Wright kept the game rolling even after that had expired.
Sheffield United’s winner came in the seventh minute of extra time at Bramall Lane, to the frustration of Taylor.
“I am a little bit disappointed with the time added on,” said the Gills boss.
“I am not saying six minutes was wrong but we were already a minute into it when the fella (Mr Gratton) put the board up. That means we’ve had seven minutes and 17 seconds. I can’t (understand where it came from) but I can’t do anything about it.”
That goal meant the Gills left Sheffield with nothing to show for their efforts.
Earlier, the Gills looked as though they could snatch all three points, thanks to Luke Norris' goal against the run of play.
Gillingham had defended valiantly for most of the game but United equalised three minutes later before snatching it with almost the last kick.
Taylor said: “The boys worked as hard as they possibly could and with a little bit of luck we could have got something out of the game.
“Of course, we are extremely disappointed with the lateness of the winner for them, but they are a very good team.
“We had a game-plan and we have to do that because Sheffield United are promotion favourites and rightly so. But I thought the boys gave everything they could for the cause and I thought we deserved to get something out of the game.
“I know that they had more chances, i understand all of that, but that is what is going to happen a lot with teams that come to Bramall Lane.
“There has never been a lack of effort all season and the players are working extremely hard for each other and themselves and I have no complaints whatsoever on that.”