Steve Evans said the ball went out of play in the build-up to Plymouth’s winner but had no complaints with the result.
Gillingham looked set to hold on for a point after being overrun in the second half at Home Park yesterday.
But they wound up empty-handed when Luke Jephcott scored for Argyle in the 88th minute.
“The ball’s actually left the pitch,” said boss Evans. “The assistant referee never sees it, right in front of us, but we should still defend it better than that thereafter so no complaints.”
Gillingham enjoyed the best of the first half but had their work cut out after the break as Plymouth turned up the heat.
Evans said: “I think we’re the better team in the first half, we miss a couple of good chances.
“I think we stifled a really good team and we’ve worked the ball into good areas. The goalkeeper made a good save and they’ve blocked a couple of goalbound efforts. That’s the first half.
“Second half, they were much better than us, they ran over us in certain areas and they deserved comfortably to win the second half.
“If you take the balance of the game, I think they were much more dominant second half than we were first half.
“We changed shape three or four times. We were under attack from the Plymouth lads.
“You take real hope from the first half. If we score in the first half the outcome can be totally different but overall they had more dominance in key areas than we did.”
Gillingham tired in the second half and it will take time to find peak fitness after a disrupted pre-season.
Evans said: “Listen, I think everyone knows we’re limited in our options today. We’re asking lads to stay on the pitch 90 minutes who’ve got no more than 70, but the option is to bring academy lads on.
“It’s different to beating Crawley, with all due respect, and coming here and playing at Home Park, it’s a totally different standard you have to play at.
“We’ll learn from it, we’ve got to learn from it and move on quickly because this league is unforgiving, as most are.