The Argentine put his side ahead in the 21st minute but goals from Ilkay Gundogan (two) and Kevin De Bruyne inflicted their first defeat in Europe this season.
Frustrations reportedly spilled over in the players' tunnel following the game, with Messi calling an unnamed City player "stupid".
SUBMIT AN ARTICLE
Apply to become a GMS writer by signing up and submitting a 250-word test article: https://gms.to/haveyoursay5
Quite why the Barcelona striker was so furious after the final whistle is largely unknown, though it's believed he was provoked as he walked off the pitch at the Etihad Stadium.
A fresh update has since emerged, detailing exactly what happened in the tunnel.
According to Cadena COPE, per the Mirror, after calling the player "stupid", Messi followed him towards City's changing room while yelling "come back here, don't hide".
International teammate and close friend Sergio Aguero then stepped in, ushering Messi away from the altercation and playfully slapping him on the chest to calm him down.
As previously mentioned, it's unknown who exactly the 29-year-old was attempting to confront.
Barcelona manager Luis Enrique will likely be disappointed by Messi's actions, especially so following a defeat that came as a result of defensive mistakes.
The Spaniard praised City for taking advantage of his side's mishaps but pointed towards Gundogan's equaliser from Sergi Roberto's error as the turning point.
"We played 40 spectacular minutes, especially on this stage against a top rival," Enrique said in a post-game press conference, per ESPN. "But we committed a key mistake and that hurt us because we are not machines.
"It's a shame that we have made that error for the first goal and from there on we had a tough time.
"When you concede like that, it's normal that you have a bad spell. During that moment we wanted to continue to dominate the game, but it wasn't possible because of errors we made and pressure from City, too.
"We didn't have much of the ball and City took advantage of our errors. We just couldn't control the game in the same way and the result reflects that: first 40 minutes for us, the rest for them."
More to follow on Messi's tunnel row...