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The goals were the difference on Saturday, said Gills boss Steve Lovell.
He felt his team were a match for Luton on the day but lacked the cutting edge.
“We deserved to get something out of it,” he said.
Report: Gillingham 1 Luton Town 3
“The crucial things are the goals. Apart from those three goals I can’t remember Tomas Holy (the Gills keeper) having proper shot to save all game, that was the disappointing and frustrating thing.
”You can work and you can run and you can create things but at the end of the day it is the score that counts. We lost the game 3-1 but as a coach and a manager you have to take the positives out of it because if you don’t then nobody else will.
“They kept going right to the end. We changed it (making three subs on the hour) and we got it to 3-1. Had we got it back to 3-2 I think we would have got something out of the game but fair play, they are a good side and up there for a reason.
“They were holding on at the end, Nathan (Jones, the Luton manager) kept asking ‘how long to go?’ and getting a bit panicky at the end. We kept going but it wasn’t to be.”
The Gills were trailing 1-0 at the break but two goals in a 13 minute spell midway through the second half for Luton left the Gills up against it.
Lovell said: “They were obviously going to get at us on the counter because we were taking chances. Apart from the goals there wasn’t a lot in the game but that is what wins games.
“In the second half we were in their half more than we were in ours. We had a lot of balls in wide areas that we got into the box but nothing came of them.”
The third goal that Gillingham conceded came from Harry Cornick run, covering most of the length of the pitch, outpacing Darren Oldaker.
“DJ will learn,” said the manager.
“You pull his shirt or you kick him into the stand, you take a booking. He probably never had that in his mind, being honest and a young boy, he wanted to try and win the ball but he was never going to get there because Harry Cornick is pretty quick.
“If we had scored that goal we would have said ‘what a great goal and a great run’ but it is disappointing that it came from our free-kick.”
Overall Lovell said his side were “defensively sound” and added: “Anybody at the game wouldn’t have thought there were so many places between us in the table but they will be happy going home with a 3-1 win.”