Tv pictures looked as if it would display Aguero pushing a supporter and he later claimed he used to be spat and sworn at.
Each golf equipment were charged through the FA for failing to keep watch over their gamers after Fabian Delph used to be sent-off.
However no particular person gamers or personnel will face any disciplinary motion.
Delph’s first-half purple card resulted in a heated argument between Town boss Pep Guardiola and reverse quantity Paul Prepare dinner within the tunnel on the destroy, however the FA stated “no misconduct came about”.
The golf equipment have till 18:00 GMT on Friday to answer the fees, whilst Aguero has been “reminded of his duties”.
Wigan and Town have additionally been requested to offer their observations to the FA through Monday, after crowd hassle on the finish of the sport, which noticed fanatics invade the pitch.
Some supporters on the DW Stadium ripped out promoting forums and threw them against police.
Police say two arrests have been made on suspicion of affray after an incident out of doors the bottom.
Chairman David Sharpe says Wigan will paintings with the FA and police to review the pitch invasion.
Will Grigg scored the winner as League One Wigan beat Town 1-Zero and ended their hopes of profitable a Quadruple of the Premier League, FA Cup, League Cup and Champions League.
It’s understood Aguero is thinking about felony motion in opposition to a fan who faced him.