Ward gave the Seasiders a spot kick two minutes into overtime, after Matthew Bates was adjudged to have handled the ball.
City themselves had taken the lead from the penalty spot just nine minutes from time, Steve Davies firing the Robins ahead.
But McInnes was more concerned with the penalty his side conceded, denying bottom-of-the-table City their first win since mid-September.
He fumed: "I just don't see how the referee could have been sure Matthew handled.
"I have watched the incident five or six times and I still can't tell whether it was a penalty.
"My understanding is that officials have to be sure so I think we have been hard done by.
"I also felt there was a foul on one of our players in the build-up.
"It hasn't been an easy time for anyone associated with the club but there were a lot of positives to take out of today's game and it is something to build on."