The match finished 1-1 after Besart Berisha scored in the first half, only to see his goal cancelled out by Wanderers' super-sub Brendon Santalab, who equalised in the last minute.
But much of the post-game discussion centred around a group of Wanderers fans, who let off a number of flares around a quarter of an hour into the match.
Referee Ben Williams had to stop play to wait for the smoke to clear.
FFA chief Gallop hit out at the offenders and said the governing body will take action in due course.
"The behaviour of some fans and in particular a section of the Western Sydney Wanderers fans at last night's match was unacceptable and will not be tolerated," Gallop said.
"FFA is currently compiling all reports from Victorian Police, stadium security and both clubs before deciding what action to take.
"This is a clear reminder of the type of people we do not want in our game and that will be reflected in the final outcomes of our enquiries.
"FFA is currently undertaking a review of the security and banning procedures to ensure a fair process for fans who are identified as misbehaving but will not waver from protecting the safety of spectators.
"Finding that balance during the banning process is central to our review but last night's events should be a reminder that the actions of a minority can damage the reputation and image of the game. That is why we will continue to identify and ban troublemakers."
Wanderers chief executive John Tsatsimas released his own statement slamming the misbehaviour.
"Those who engaged in the display of flare and railway detonator ignition at last night's match have no place in our club," Tsatsimas said.
"Let us be quite unequivocal: those who engage in activity that is illegal, which has time and time again been clearly spelled out as not acceptable in an Australian football venue, do not have our support.
"You are not part of our club."
