The Dons were aiming for a seventh straight win after booking a Betfred Cup final place against Celtic with a 2-0 win over Championship side Morton at Hampden Park on Saturday.
However, Alex D’Acol derailed the Pittodrie bandwagon when he scored from the spot in the sixth minute after Collum adjudged him to have been manhandled by Anthony O’Connor.
McInnes said: “I thought it was very soft and having watched it again I don’t believe it’s a penalty.
“I spoke to Willie about it after the game and he’s obviously seen it differently which can happen.
“He says he’ll look at it again, but there is no contact there.
“For me, D’Acol has backed in and my player has done nothing wrong, there’s no infringement there, and I think it’s very harsh to have a penalty against us.
“And if that’s a penalty, then when Kenny McLean gets hauled to the ground near the penalty spot that was even more of a penalty.
“Sometimes they go for you, but the referee sees it differently. He may well view it differently when he sees it again.
“We move on though, referees can make mistakes but the game is done now.”
Despite his frustration at the penalty award McInnes says his side were “more than good enough to get something”.
“We expected Hamilton to play in the manner they did, they came out of the traps quickly and I felt we had to be more aggressive early on,” he said.
“I think the goal helps them and galvanises their cause, but we finished the first half well and created a few chances.
“While they broke away in the second half and had a couple of opportunities, we changed our shape and I thought we were far better and dominant in the second half and deserved something for our efforts.”
McInnes was pleased with the news that the Pittodrie club will get a 50-50 split of the tickets with Celtic for the Betfred Cup final at Hampden on November 27.
He said: “I believe we have actually nine or 10 more which is even better.
“I am delighted as I think common sense has prevailed.”
Accies’ first win in six games took them into sixth place but player/manager Martin Canning, while delighted with the three points, remains cautious.
He said: “The league position at this stage isn’t important to us.
“We’ve got to try to work hard, play well and continue to pick up as many points as we can.
“Our biggest aim is to stay in the league and if we can achieve that, it’s been a good season for us.
“If we can pick up points to take us further up the league that’s great.
“We’re sixth tonight but in two weeks’ time it could be second bottom as it’s so tight.”