Referee Declan Bourne penalised Greg Docherty for handling Matt O'Riley's powerfully-struck effort inside his own box with 10 minutes of Saturday's League One clash remaining, and Scott Fraser did the honours from 12 yards to settle the contest.
And, while the Northern Irishman accepted the match official's decision, he argued that his team were unfortunate not to get two penalties of their own.
"I think in the season things happen where things go against you. It's gone against us today a little bit with the two penalty decisions that we should have had at one end and then two or three minutes later they get one," McCann said.
"I think it was [a penalty]. Obviously I am disappointed that it went their way but I think it that's the law of the game now that if a hand is out then that's a penalty.
"But, what I would say is that we had two very similar two or three minutes before that. George Honeyman had a shot in the box that was blocked by their centre-half with his arm out and then again another shot from Greg Docherty, I believe, that [Dean] Lewington blocked with his arm as well.
"It's disappointing that it went against us, but I think it was a penalty.
"They are all penalties, in my opinion. That's the new law of the game, if your hand is raised then it is a penalty."
City created enough chances on a freezing cold afternoon in East Yorkshire to have had the game sewn up before the Dons' late goal, but for the third match in succession, they failed to get on the score-sheet.
The Tigers have now registered just one solitary goal in their previous five League One outings, and while McCann said that his players need to rediscover their "mojo", he insisted that he would be more concerned if they weren't carving out opportunities in the first place.
“We’re going through a spell at the minute. As a team, we’re snatching at chances," he added.
“As the manager, as staff, as players, we’d be worried if we weren’t creating the opportunities. But we are creating the opportunities, we just don’t seem to be finding the back of the net.
“We’ve gone from scoring seven goals in two games against Accrington and Portsmouth to one in five. That’s just how it’s gone for us.
"These are things that are happening to us at this present time and we’ve got to try to find our mojo. We’ve got to try and find our mojo back."
Hull remain second in the League One standings despite Saturday's defeat.