Gabriel Jesus had already put the champions in front at the Etihad Stadium on Monday when Boly was dismissed by referee Craig Pawson in the 19th minute.
Boly appeared to win the ball as he made a forceful challenge on Bernardo Silva, but the defender caught the City midfielder's ankle with his studs on the follow-through.
And Nuno had no arguments about Pawson's decision to send off Boly, who scored a goal with his hand as Wolves drew 1-1 with City at Molineux in August.
"It's very close to me and I think it's a clear red card," the Wolves boss told a news conference.
"Not only the red card changed the game, but the way we conceded with a long pass. The red card makes the task much harder.
"You know it is difficult to stop them but you try to avoid certain situations - and it was a 30-yard pass so we must improve.
"But you do not make a game plan with one less man."
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Nuno hopes Wolves can learn a lesson from their loss to City, Jesus adding his second goal from the penalty spot before a late Conor Coady own goal wrapped up the scoring.
"Sad, disappointed, we have to look at the game, knowing what happened," he said. "We started well, we conceded a way we shouldn't.
"Then the red card, you stay in the game but City with their speed, we have to be realistic. The only positive is to say it was an experience, it can happen.
"With one man less, the game still has something to do. We have to improve. we knew it was tough and it became harder."