Video circulated on social media showed a fan outside Suncorp Stadium on Sunday during Brisbane Roar's 3-2 win over Melbourne Victory being restrained by two police officers and a security guard.
The supporter can be heard screaming: "I can't breathe".
It was one of several flashpoints between fans and security officials at games over the past weekend.
Western Sydney Wanderers active supporter group the RBB (Red and Black Bloc) staged a walkout during Saturday's 4-1 derby loss to Sydney FC where there were 14 arrests.
Supporters posted videos of them being surrounded by NSW Police after exiting CommBank Stadium and one Wanderers fan uploaded images of cuts to his face, which he claimed were as a result of police activity.
Sources say the RBB were returning a club-authorised banner which was unfurled prior to their game and attempting to return to their allocated seats when a large group were told they could not return.
Macarthur fans also clashed with security guards who forced them to take down a banner in Friday's 2-0 home win over Melbourne City.
Further footage distributed online following the Brisbane game appeared to show police pushing Roar supporters as they made their way to the venue.
Queensland Police said on Monday they issued a 17-year-old boy and a 27-year-old man "with move on directions following alleged anti-social behaviour" while a 16-year-old boy was arrested for the alleged lighting of a flare at the Roar-Victory game.
APL commissioner Nick Garcia was unavailable for comment, with the league body issuing a two-paragraph response confirming they were investigating the incidents.
"Creating a safe and enjoyable environment both inside and outside our venues for all fans, stakeholders and staff is our number one priority," the APL said in an unattributed statement.
"We are aware of incidents that have occurred at CommBank Stadium and Suncorp Stadium, and are investigating these incidents as part of a full review with clubs, venues and police, along with feedback from fans."
