The Italian’s appearance in the FA Cup fourth-round replay on Sunday was his first start in almost two months following a spell out with a knee injury.
As he walked off the Eastlands pitch, Balotelli threw down his snood before trudging down the tunnel, but Mancini has no problem with the former Inter Milan youngster.
"We decided before the game to replace him after an hour," said Mancini. "It's his first start after injury and he had a clash of heads.
"He was unhappy but I will explain to him in a couple of days.
"It's not a problem. We want him fit for the next two months as we have a lot of games.
"He played well and didn't have any problems with his knee.
"We want to ease Mario back into action. He knew he would not play the full game. Sometimes in training when he misses a chance he holds his knee and then when he scores he doesn't!"