Rovers' late bid to sneak a place in the League One play-offs suffered a setback as a recent nine-game unbeaten run was brought to an end on the back of a 3-0 defeat at Gigg Lane.
But Darrell Clarke's side had been forced to play for almost an hour with ten men after Toner dismissed Sinclair for two separate incidents of simulation.
The referee also irked the Bristol Rovers manager for a failure to spot a handball in the phase of play directly leading up to Bury's second goal and for a failure to deal more severely with goalkeeper Joe Murphy following a coming together with striker Rory Gaffney in stoppage time.
Stewart said: "I have seen the footage back and I can say that the first incident is not a dive.
Match report
"The second one maybe, but a red card was very harsh on Stuart. We all know what sort of guy Stuart is and for him to get sent off for two dives when one of them wasn't is very disappointing.
"Stuart could have been a bit careful with the second one, but in the heat of the moment it is sometimes difficult to make the right decisions. He didn't do that and that is just one of those situations you have to learn from.
"I haven't seen the penalty decision back again but it looked soft in real time. I hope the referee looks back at the footage to see if he made the right decisions or not.
"I have to self-analyse as a coach and I hope the officials will do the same. There were eight bookings in the game and it wasn't that sort of game. It was a very strange night."
Clarke missed the post-match briefing as a result of requesting a summit with the official some 30 minutes after the final whistle, and Stewart added: "It is about discussing differences of opinion like adults and hoping that we get some of our questions answered. That is all you want. You go in there to get the truth and if you disagree, you disagree.
"At least you have got something off your chest in the right way. If the referee learns from it and it helps him when he takes charge of our next game then that is great for everyone."
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Rovers remained four points off sixth-placed Millwall with eight games of the campaign remaining.
"The red card changed the game," Stewart said. "The score-line is not a fair reflection of our performance. They didn't have lots of sustained pressure on our goal and we still attacked their goal in the face of having to play at a numerical disadvantage for almost an hour.
"That made it quite difficult. Players are always going to make bad decisions under pressure. That's the way it is when you are chasing a game and you leave yourself three on three at the back. It is also important that the officials deal with the pressure as well.
"I'm not sure that was the case tonight, but we all make mistakes. We are all human and it is nice if people hold their hands up. I am disappointed with the result but I am not disappointed in the way we played.
"We kept trying to attack their goal in the second-half. We had some good moments. We hit the post and we forced some good saves out of the goalkeeper."
Rovers will check on the fitness of James Clarke, who was substituted with a suspected asthma-related condition, and Rory Gaffney, who broke his nose, before they entertain Chesterfield at the Memorial Stadium on Saturday
Read more at
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