It is claimed that a supporter hit the Argentine from behind, spat at him and said “suck my d***” during a pitch invasion.
Hundreds of Wigan supporters flooded the pitch at the DW Stadium following the Latics’ dramatic 1-0 victory.
A small number, however, jostled with Aguero, forcing a reaction from the Argentine.
The incident is one of several which is currently being investigated by the Football Association. Charges could be brought on Wednesday.
English football’s governing body have asked both City and Wigan for their observations on a number of issues, from security arrangements and policing to the behaviour of their players and coaches.
City have been in contact with their lawyers as part of the process and Goal has learned that the club could sue the fan they believe provoked Aguero.
City are also planning to speak to Wigan about their handling of the match, as they are unhappy that so many fans were able to get onto the field of play.
Wigan vowed on Tuesday to carry out a full investigation.