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With the game goalless and a minute to go until half time, midfielder Kasey Palmer went down inside the area after having his shirt pulled by Jamie Sterry for a dubious penalty that Callum Marshall tucked away.
After the break Jamie Donley scored twice before Bayley McCann grabbed a late consolation, but McCann said: “I think we’ve been done by a poor decision from the referee.
“There was nothing in the game, first half we were quite good, had a real good chance early, Neill Byrne has got to score, he knows that, it’s a free header, you need to take those opportunities.
“Then the one big decision in the first half goes against us. Kasey Palmer dives in the box and the referee gives a penalty. There’s no point me sugarcoating it, that’s what happens and it’s really disappointing we’ve been undone on that, particularly coming away from home to a place like this which is tough.
“That was disappointing and in the second half we never got going. Luton were better than us for 25, 30 minutes, we struggled but I felt that decision gave them momentum, and we struggled after that.”
Following Byrne’s close-range header that flew over, Marshall was also narrowly wide, before Town were awarded their spot kick in the latter stages, Marshall making no mistake.
The second period saw Hatters take control, Jamie Donley firing into the bottom corner from Jake Richards’ pass on 51 minutes and then doubling his tally when Richards’ cross was not cleared with 72 gone.
Town had other chances with Marshall off target twice, as were Donley and Tudor Mendel, before McCann looped his header in for a first Rovers goal with six minutes left.
Hatters boss Jack Wilshere added: “I thought the players found a way in the first half. They make it difficult for you and we had to get hold of that, and find our way in the game which can happen after a big performance on Saturday (beating Leicester 2-1) and the game ends in the way it did.
“It takes a lot of emotional energy, players have to go again, and we need players that can do that as that is the demands at this level, but it’s not easy, I know that from my experience as a player.
“I’m happy for the players and proud of them for that, because we found a way in the first half.
“I thought we deserved our lead at half time, and then that was the message, if we go to the next level we can take this game away from them, so credit to the players as that took a lot.”