In ugly scenes at the DW Stadium, Wigan fans charged onto the pitch at full time with some taunting the Premier League leaders.
Aguero appeared to try and shake off a mocking fan after an altercation.
And he had to be dragged away after trying to get at the supporter a second time.
BBC pundit Alan Shearer said of the incident: “You don't know what he's done to Sergio or what he's said to him.
“It's not nice when the fans come on the pitch and say stuff to you so let's hope everyone is okay."