Marriner chalked off a goal from Gary Madine at the death when Miguel Llera had protested too strongly for not awarding a penalty in the build-up.
Llera, who had put Wednesday ahead in just the second minute before giving a penalty away, was booked for his actions which stopped play before Madine's effort crossed the line, though he is denying touching the Premier League official.
McInnes accepts Wednesday could have had a penalty when there appeared to be a handball and said: "I think the ref has a decision to make on the handball.
"But he gives a free-kick prior to the ball going in the net, my players have said they heard a whistle before the ball went into the net.
"For me the only thing I have seen is the over-reaction of the centre-back grabbing the referee with both hands, it was over-aggressive.
"You can't manhandle the referee, he is quite within his rights to give a free-kick, that's a fact.
"Whether Sheffield Wednesday might have had a penalty before that is another matter, but before the shot came in the referee's whistle had clearly gone.
"The complaint they should have is whether it was a penalty or not. It could have gone either way."