Footage showed the Argentine raise his hand after being taunted by a Wigan fan before he was led off the pitch by City staff.
Objects including an advertising board were thrown at police and stewards from the stands and, according to Sky sources, Man City want answers from Wigan as to how so many fans encroached onto the pitch and got so close to their players.
"Emotions always run high at football matches and sometimes this means that officers have to intervene to ensure the safety of the fans". But I don't like to see this at the end of the game. "I don't like what I am seeing here".
Fabian Delph was sent off for the visitors just before half-time and the League One side took advantage when Will Grigg prodded home the victor 10 minutes from time. I don't think Pep and his bench thought it was but that's football.
The striker's low finish capped a night of drama at the DW Stadium, with City's Fernandinho wasting a fine chance shortly before Delph was dismissed for a heavy challenge on Max Power.
Wigan survived a nervy finish, with the final whistle prompting a pitch invasion. "We hope he goes on and wins Champions Leagues and Premier Leagues because they deserve that".
When City next threatened, after Stones headed down Delph's cross, Fernandinho's shot rose over by some distance when he looked certain to score.
Grigg kept his cool after an error from Kyle Walker in the 79th minute to slot beyond Claudio Bravo and book a quarter-final place for Paul Cook's League One side, ending Pep Guardiola's quest for a historic quadruple in the process. "To beat a Man City team you have to do that".
The Premier League leaders were stunned by the League One side in the fifth round.
Cook also didn't wish to dwell on the incident, telling reporters: "I felt at the time it was a straight red".
As we wrote yesterday, the City manager has made it his personal mission this season to call attention to the number of unsafe tackles that players get away with on a regular basis.
"But the conversation about the game shouldn't be about that - it's a great night for Wigan Athletic".
"I didn't have the feeling that we didn't try", said Guardiola.
The result marked the end of City's bid for four trophies this season, and Guardiola played down the significance of the red card.