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Justin Edinburgh admitted he was at a loss to explain why defender Josh Pask handled in the box on Sunday.
The incident led to Sheffield United getting a penalty, which they scored to win the game 2-1.
Gills boss Edinburgh said: “It’s a disappointment (to lose) but you can’t legislate for that incident and Josh was absolutely distraught.
“He will never do that again in his career but in that split second, you don’t know why you do it. Why would he do it? People with football intelligence understand those things happen. Why? Nobody will ever know and he won’t know.
“It’s an instinctive decision and that won’t be the last time you see that happen, for or against.”
It was one moment of many that didn’t go right for the Gills.
Edinburgh said: “We needed to make better decisions throughout that game.
“We knew Sheffield would come onto us, looking for that winner, but I felt we just played into their hands.
“I don’t think there were a lot of clear cut chances. We probably had the better chance, at 0-0, Cody went through after good play. That is what we needed to do. We knew they would play high and the space was in behind, but we just continued to come up short in getting behind.
“When we did play down the sides or in behind them we were always going to be a threat. I never felt threatened. It was a great goal for the lead, we could have always nicked another one, but it was a controlled performance, if not perhaps spectacular.
“At 1-1 I thought that was going to be the result and I think both managers would have settled for that. Cruelly for us we have been defeated.”