Security were forced to extinguish two flares dropped in the middle of the Wanderers' active supporter bay at ANZ Stadium during the second-half of Western Sydney's 4-0 loss to rivals Sydney FC.
The FFA have said they will review security footage of the incident but have indicated it is unlikely they will impose the suspended three-point penalty and $50,000 fine punishment handed down to the Wanderers in February.
Meanwhile, football fans and media commentators have called on the governing body to take a firm stance on crowd behaviour.
Many Wanderers fans also took to social media after the match outraged at those responsible for the flares.
"I am a WSW member and I am a sick of the selfishness shown by a tiny minority. The RBB need to help weed out those who keep letting off flares," Wanderers fan Kevin Skelley said on Facebook.
It was a sentiment shared by fellow Western Sydney fan Debbie Smith, who demanded the club intervene with the running of the Red and Black Bloc supporter group.
"I think we need to disband the RBB and start again. These guys condone flares and let the perpetrators get away," she said.
On Friday, the Wanderers released a statement to fans which condemned the use of flares at matches.
Last season a group of Wanderers fans ignited more than a dozen flares, as well as crowd-frightening detonators, during a match against Melbourne Victory at Etihad Stadium.
A week later, Victory were also punished by the FFA after poor behaviour at the Melbourne derby, including two flares being ripped, missiles thrown onto the pitch and a TV news crew allegedly assaulted outside AAMI Park.
At the time, the FFA said similar incidents would trigger the suspended sanction and see a points deduction.
Five year bans were also threatened for fans caught using flares after Greek supporters ignited close to 30 before and during their June international match with Australia at Etihad Stadium.