The Australian Professional Leagues (APL) confirmed to AAP they were investigating the incident.
Sydney FC won the derby 4-1 but by half-time the RBB had exited the stadium.
NSW Police released a statement on Sunday morning saying spectators had earlier gathered at Prince Alfred Park and marched to the stadium, during which several flares were ignited and two people were refused entry.
Police had then assisted security at approximately 8pm after a fight broke out on the concourse area of the stadium. There were no reported injuries.
A 37-year-old man was ejected and issued with a ban notice and the RBB had walked out in support of him.
"As a result of the police operation, 14 people were ejected, six of which were issued banning notices," said the police statement said.
"Two people were issued an infringement notice, one for offensive behaviour and a second for igniting a flare just before full-time.
"Inquiries continue with further action expected in relation to the possession and igniting of flares before and during the match."
A lit flare could been seen in a bay containing Sydney FC supporters.
A flare was set off during the Sydney ALM derby clash at Commbank Stadium. (Dean Lewins/AAP PHOTOS)
Various reasons have been given by fans on social media site 'X' for the RBB walkout.
There was widespread discontent with a "heavy-handed" police response, with one supporter saying the police action was taken because "they (RBB) tried to go back into the bay after holding banners in other bays".
Another suggested there was dissatisfaction with the officiating.
Police said they took action to "ensure the safety of players, officials and thousands of spectators attending an A-League match".
An (APL) spokesperson provided AAP with a statement on Saturday night's match.
"We are aware of an incident that occurred inside the stadium during the first half," the spokesperson said.
"We are working with all parties to investigate the matter as part of prescribed protocols."
AAP contacted the Wanderers who pointed to the APL statement in response. Sydney FC declined to comment.
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