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Maidstone boss Jay Saunders felt there was little chance of Tranmere’s late winner being ruled out in front of such a big crowd.
Steve McNulty struck for Rovers nine minutes from time after Stones keeper Lee Worgan flapped at a corner at the giant Kop End.
There were suggestions Worgan was fouled but referee Anthony Blackhouse allowed the goal to stand and the majority of the 4,797 fans went home happy as Rovers won 2-1.
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Saunders said: “I didn’t think coming here we were going to get a lot out of the ref, any 50:50 decisions seemed to go Tranmere’s way, which you kind of expect.
“Worgs felt he was being fouled, I think there were a few people saying, but he’s never going to give that, especially at that end with all the supporters behind him.”
Saunders was more frustrated that Maidstone conceded the corner in the first place.
He added: “It’s annoying the second goal because if we clear our lines and deal with it at source the corner doesn’t happen and we maybe go away with a point but Tranmere are a very good side. We just have to take it and move on.”
Tranmere went into the game top of the National League with four wins out of four.
They bossed possession and led at half-time through Andy Cook but Stones levelled with Alex Flisher’s goal just after the hour, only to miss out at the end.
Saunders said: “It kind of went how I thought it would. I knew they’d have quite a lot of possession, they’re obviously a good side, full-time, one of the biggest sides in the league, so we knew it would be tough coming here.
“We wanted to try and frustrate them first half if we could and try and hit them on the break at times. I’m just disappointed with the goals again.
“I felt we could hurt them on the break. They were pouring men forward where they had good possession so I felt if we could be solid and not concede again then we could hurt them and we obviously got the equaliser.
“Then I thought we had a 10-minute spell where we looked like we were getting some good chances and causing them problems but we didn’t take one of them and then a sloppy mistake again has cost us.”
Two-hundred-and-two Maidstone fans made the 540-mile round trip to Prenton Park and gave the visitors magnificent backing.
Saunders said: “I thought they were brilliant. I thought they completely out-sang Tranmere. They’re fantastic. They’re like it every time we go away and it’s fully appreciated. I know it’s a long trip, I’m just gutted we couldn’t get that point for them.”
Read the match report from Maidstone's 2-1 defeat at Tranmere