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Steve Lovell felt his Gills team did enough to take all three points from their visit to Plymouth.
Gillingham ended up leaving with nothing after bottom side Plymouth won it in the last minute.
Manager Lovell said: “We dominated the game in the second half, no doubt about it, when we got the equaliser I really thought we could go on and win it.
“We were on the front foot, we were creating chances and getting set plays. I am just gutted for the boys because they deserved to get something out of it and not just a point, they deserved to win the game.
Report: Plymouth Argyle 2 Gillingham 1
“I am sure anyone at the game would have said the same.”
The Gills could have led the game early on but Tom Eaves was denied a goal despite the ball seemingly crossing the line.
“I couldn’t tell from where I was,” said the Gills boss.
“But our forward Tom Eaves is the most honest person you are ever likely to meet and he was adamant it was over the line, Josh Parker was the same.
“That is twice in a week (after Parker had one ruled out against Oxford) but it is gone, it is no point harping on about it.”
Eaves was also at the centre of the two crucial moments at the end of the game, hitting an equaliser on 87 minutes and then losing possession in the build-up to their winner.
Reflecting on the Eaves goal the stood, Lovell said: “It was a good finish.
“He can score goals like that but when he is in and around the box they don’t seem to fall for him or they are saved. I am just so disappointed not to get anything from the game because we deserved it.
“Tom scores a goal like that but then makes a mistake for what led up to the second goal but that is how honest he is, he is devastated.
“He lost the ball in an area between the 18 yard box and the halfway line. He tried to go the wrong way, if he turns and goes the other way then it’s safe. It is easier said than done.
"He has held his hands up and said it was a mistake. The positive thing is he won’t do it again, he will learn from it. That is something you have to take from it."