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Gills boss Justin Edinburgh had no defence for dismissed striker Rory Donnelly.
The 24-year-old let his frustrations get the better of him and reacted to provocation from the home fans at AFC Wimbledon, earning a two-game ban for offensive language.
A one-finger gesture was missed by referee Darren England but not by the linesman.
“It’s unacceptable,” said Edinburgh. “He will be punished, he knows that. He has let himself and his team down. It’s ludicrous, it really is.”
Donnelly was dismissed with just a few minutes left, having being introduced from the bench early on for injured Bradley Dack.
The ban does not count for EFL Trophy games so Donnelly will miss the League 1 matches against Oldham and Bristol Rovers.
Edinburgh said: “They are the things sometimes players don’t think about. It was not Rory and it summed up the frustrations which we felt out there.”
The striker later apologised for his actions. He said: “I want to apologise for my performance and the actions that followed, leading to my dismissal from the pitch.
“I let my emotions and passion for Gillingham get the best of me and it was an inexcusable, spur-of-the-moment reaction, which I deeply regret. I want to apologise to my team-mates, the club, management and fans who I have let down.”