Mess opened goal for Barcelona before Ilkay Gundogan (two goals) and and Kevin De Bruyne scored to give City a 3-1 win at the Etihad.
After the game, the Barcelona star was said to have been furious with a City player who said something to to his ear.
According to Spanish newspapers Marca and Mundo Deportivo, Messi even headed into the Manchester City dressing room to confront the player.
Mundo even reports that Messi headed to the City dressing room to look for the unnamed player.
“Stupid, come here and show your face, don’t hide,” Messi allegedly told the City player durng the altercation.
His International teammate Sergio Aguero was said to have waded in to calm the 29-year-old.
Reacting to the incidence, Aguero who grabbed an assist for City in the 3-1 win understood that his friend was just disappointed in losing the game.
“I saw him there, he was feeling bad. I know him well enough to know when he’s bad when he’s good. But when you lose, nobody’s good,” Aguero told reporters.
“[I saw] nothing. I thought Messi said something to me but he didn’t, and then we [the other players] talked about other stuff.
“[It was] nothing serious. I heard something but I don’t know what happened.
“When someone loses you have to respect them. Leo wasn’t in the mood to talk and I respect that.“