The club on Tuesday announced it will close its active supporter area for Sunday's match against Perth Glory at Spotless Stadium.
"Unfortunately a small group have made this action unavoidable," WSW chief executive John Tsatsimas said.
FFA said it would take into account the Wanderers' initial response to the incidents and "any other measures it takes" before the governing body makes a determination.
The Wanderers have only just escaped a suspended points penalty that hung over their heads last season for flare-related indiscretions, among other offences.
In February 2016, the Wanderers were fined $50,000 and had three competition points suspended for bringing the game into disrepute after 25 flares were lit outside Melbourne's Etihad Stadium.
The suspension was due to expire in February 2017 but was extended for a further three months when more flares were lit at the Sydney derby early in the 2016-17 season.
Tsatsimas delivered a final warning last July to a "rogue element" of the RBB, threatening to shut them down should any further "illegal and highly dangerous" incidents occur.
AAP
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SYDNEY MORNING HERALD
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