Justin Edinburgh admitted the two red cards shown to Rochdale players had a negative impact on Saturday's game at Priestfield, which the Gills won 1-0.
Referee Andy D'Urso sent off Dale keeper Jamie Jones for bringing down Cody McDonald outside the box and just six minutes later, his red card was out again.
Matty Lund was dismissed for a bad challenge on Bradley Dack, whose 14th-minute header turned out to be the winning goal.
Gills boss Edinburgh said: "We’re obviously delighted with the three points.
"It was difficult circumstances, particularly in the second half, but I thought we started the game really well. We got the goal and it was a very competitive first half.
"The two sendings-off disrupted it. We lost our rhythm and we didn’t punish Rochdale enough - but credit to them, they went at it and they had nothing to lose.
"Sometimes it’s easy when you’ve got that scenario but we certainly should have dealt with the football a lot better than we did.
"All in all, it’s three points and another clean sheet at home. There’s some positives to take out of the first half but once the red cards have been produced, the game lost its way."
Edinburgh was asked after the game for his opinion on the two dismissals.
He said: "I haven't reviewed them myself because it wasn't affecting us.
"For the first one, I didn't think the keeper got anything (on the ball) but I haven't viewed it again. I think the second one was harsh, a yellow card would have been sufficient.
"It's a difficult job. The referee has to make that decision instantly and he's given the decision on what he's seen."