Michael Flynn said Swindon need to stop giving points away if they are to sustain a promotion challenge.
Connor Mahoney’s first-half goal earned Gillingham a 1-0 victory as the Kent side leapfrogged their rivals into the League Two play-off places.
Flynn said: “We have to stop throwing points away.
“We have absolutely dominated the game, but we gave away a poor goal. We know that Mahoney is left-footed and we have let him cut in on his left, nobody put any real pressure on him.
“The chances we missed were poor, they should have been in the back of the net.
“We have missed a header from three yards and you don’t see the Wrexhams and the Stockports missing those kind of chances.
“Wrexham have gone and scored an 89th-minute winner again today – that can’t be just by luck, that is about belief, it is about being clinical, and it is about a winning mentality.”
Gillingham ended a barren run on the road with a first away win in five.
The visitors took the lead midway through the first period as Mahoney came inside from the right and drilled the ball low and a deflection wrong-footed keeper and namesake Murphy Mahoney.
Swindon were almost level moments later when Dan Kemp clipped the ball into Jake Young, whose powerful volley was spectacularly saved down low by Jake Turner.
Swindon’s Charlie Austin turned a corner just wide and Murphy Mahoney denied Macaulay Bonne one on one at the other end. Gillingham could have put it beyond doubt when they won a 74th-minute penalty after a foul from Harrison Minturn but Cheye Alexander stepped up and side-footed it well wide.