Leo Bonatini’s 12th goal of the season secured a 1-0 victory at St Andrew’s on Monday, a sixth straight win for the in-form leaders.
Harlee Dean was dismissed late on for Birmingham after pushing Diogo Jota to receive a second booking but Wolves were cruising before the red card.
Jota was targeted by the hosts, including with one early tackle from Marc Roberts which earned a booking, and Nuno felt Blues crossed a line.
“I’m not against being aggressive as long as you are fair and going in from behind making a tackle in the back of a player is not being fair,” he said. “That can cause injury.
“The referee did well, he manages the game well by booking the players. As long as the football is under the law I’m not worried.
“There’s no manager saying to a player to go and kick but as long as the referee is there and does his job I’m not worried.”
But Blues boss Steve Cotterill responded, insisting Alfred N’Diaye should have been dismissed for clashing with Maikel Kieftenbeld and Stephen Gleeson.
“I don’t care what his (Nuno’s) thoughts are. He probably doesn’t care about mine and I have no interest in his,” he said.
“The red card was very weak. If he (Jota) should fall to the floor God knows what Stephen Gleeson should have done when one of their lads went head to head with Kieftenbeld.
“He didn’t headbutt him but he did give Gleeson a clip round the face. That’s a straight red. If Gleeson goes to the floor he gets sent off.”
Wolves reopened their four-point lead over Cardiff and are 10 points clear of third placed Bristol City but Nuno refused to talk about promotion.
“We’re looking at the next game at home. We only think about the next game, we don’t think about anything else,” said the former Porto manager.
Birmingham remain in the relegation zone on goal difference following a defeat where they rarely threatened.
They were the architects of their own downfall when Jonathan Grounds gifted the ball to Ivan Cavaleiro after eight minutes.
David Stockdale saved twice from Cavaleiro and Jota before Bonatini eventually scored, although he needed goal-line technology.
Cotterill added: “I’m not going to hound people for individual mistakes. We’ve made a mistake, it wasn’t a deliberate one, and every time we make a mistake we get punished.
“We were organised and Wolves were average.”