Marquis collected two yellow cards in the defeat, with the second leading to his dismissal with 40 minutes to go at Kingsmeadow.
But McCann protested the innocence of his striker - who will miss Tuesday's trip to Blackpool as a result of the red card.
"I need to be very careful what I say," said McCann, who was charged by the FA over his conduct following last weekend's draw with Charlton Athletic.
"If you watch it back, their goalkeeper has run into John and dragged John to the floor.
"He's had a silly booking in the first half. Him and Wagstaff got booked and I think the referee could easily have had a word with them and sent them away.
"And the second one is ridiculous really when you see it back.
"The goalkeeper runs into John, pulls him to the floor and John gets booked and sent off.
"It is what it is.
"I'm not getting involved in frustration with anyone because it gets me into trouble.
"He'll miss Tuesday. It is what it is. That is why we've got a squad.
"It's not nice to miss your talisman, your leading marksman."
The first yellow card incident saw Marquis push Scott Wagstaff who nicked the ball away after Rovers were awarded a free kick.
And after the break Marquis tussled with Wimbledon keeper Aaron Ramsdale who was attempting to play quickly.
Because the red card came as a result of two yellows, Rovers are unable to appeal the decision.