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Boss Steve Evans was disappointed to see his side throw away a two-goal lead but felt robbed of a chance to grab a winner.
Gillingham conceded shortly after goalkeeper Jack Bonham had saved a penalty kick and the hosts soon scored a second, to level things up.
Report: Tranmere 2 Gillingham 2
Evans felt his team should have been awarded a penalty themselves, in the final minute, when Mikael Ndjoli went to ground in the box.
The Gills boss said: “I can see why Michael Salisbury has given their penalty, but he needs to explain why he hasn’t given us one right on full-time.
“They are both very similar but the excuse from him, on the pitch, was that their centre half is big and strong. Okay, well done.”
Barry Fuller conceded Gillingham’s penalty after a tangle with Tranmere striker Paul Mullin.
Evans said: “It was rash defending from Barry, it wasn’t a challenge or a pull, he charged him a bit heavy and there was contact and I can understand, he has allowed the referee to give a decision so the referee has given it.
The Gills boss was keen to speak to Mr Salisbury with him after the game.
He said: “I know what he is going to say, ‘he’s a strong boy’ that is what he told my captain.
"I spoke to a couple of people in the tunnel and they said if he gave theirs then he has to give ours, they were both very similar.
“Mika has robbed him (Manny Monthe), he has got goal side and then he is bundled over, it’s a penalty, but at the home end at Tranmere. I will let Michael explain it.
“What I would say to the match referee, would he have given Tranmere that at that end? I don’t know the answer.
“You ask the match referee to do his job. I tried to speak to him on the pitch but he told me to go away."
Evans’ frustration led to a confrontation at the final whistle with Tranmere counterpart Micky Mellon.
“I think he misinterpreted what I said,” Evans explained.
“He said ‘why are you pointing?’ I was pointing to say, ‘if that’s a penalty, then that’s a penalty’.
“Micky thought I was pointing at him and I said to him I wasn’t. Micky is passionate like I am, I have no problems with him.”
The penalty decision aside, Evans admitted his side should have seen the game out, having led 2-0 at the break.
“It was a game of two halves,” he said.
“We were by far the superior side first half and Tranmere were in the second.
“We missed a chance one on one and one other good chance to make it 3-0 and that possibly would have been over.
“We were so dominant but you can’t give teams a lifeline, it doesn’t matter what level
“They started really well second half and we seem to have weathered that storm, we were probably having our best spell of the second half and then we give away a needless penalty away.
“We have the corner and don’t make the first contact, the goalie makes a good save, we don’t clear it and they stick it in the net
“You know what you are going to get at Tranmere, against Micky’s teams, they will come at you. They carved us a bit down that right side, our left, to get the (second) goal.
“You say in isolation a point away from home at Tranmere is a good one, but when you have been two zero up and comfortable on the hour mark, it is certainly two lost.”