The Robins had been awarded a contentious spot kick of their own in the first half, converted by Sam Baldock, and this almost secured them a vital win that would have lifted them off the bottom of Sky Bet League One.
But Cotterill's side were denied by a decision that looked every bit as soft on the day Louis Carey equalled City's club appearance record by playing his 645th game for them.
Cotterill said: "If you look at the game overall it was probably worthy of a draw, but when you get so close and have it snatched away from you, it's very disappointing.
"The two penalties, for both teams, are as soft as anything.
"If our penalty was a penalty then what he should have done is give us two penalties for the two corners before because the grappling there was far worse than the actual penalty.
"I spoke to the referee at half-time and he said: 'don't worry, I won't be evening anything up.
"Famous last words, but you're always wary of it.
"Conceding a penalty in the 89th minute is a real kick in the teeth for the lads because I think we had worked hard enough for a 1-0 away victory.
"I thought there were characteristics that will improve us - we were tougher than we have been."
City were awarded the game's first controversial penalty when Dean Leacock was penalised for holding Aden Flint, with Baldock slamming his spot kick home.
Just when it seemed this would be enough, Alan Sheehan held his nerve after Marvin Elliott had been judged to have grabbed Leacock.