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Gills boss Steve Lovell felt his side were well on their way to victory before a controversial penalty decision gave Wimbledon a lifeline.
Cody McDonald was adjudged to have been fouled by Luke O’Neill, a decision Lovell felt was harsh and one which Wimbledon took full advantage from.
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Lovell said: “I am disappointed with the result because I felt we deserved to win the game.
“At 1-0 we were well in control but they got the penalty which was from a big punt upfield, from nothing, and the referee gave it.
Report: Gillingham 2 AFC Wimbledon 2
“I thought we would win it quite easily when we went 1-0 up. The penalty was a bit harsh and the goal then lifts them.
“We got back and scored the second and again it looked as though we would go and get another couple. Then, from a set play, they get a goal.”
Wimbledon got their second from a corner, scored by Harry Forrester after Deji Oshilaja won the header from the set-piece.
“It got caught under Gabs (Zakuani) a little bit,” said the manager.
“That was the first time in the game. He has won everything all game, he and Max were brilliant, they complement each other well.
“It was just two bits of bad fortune and we get punished for them. We don’t seem to get that.”
Despite more dropped points, Lovell was taking the positives.
He said: “It is all about the performance, the levels and work rate and that is still up there, so I am happy with that.”