SPFL notices of complaint have been raised against Celtic, Partick Thistle and Aberdeen.
The league body confirmed action has been taken over "unacceptable conduct" in respect of incidents at the end of the season.
The SPFL condemned shocking incidents throughout the 2024/25 season with disciplinary action taken against a number of clubs during the campaign.
Now, Celtic, Partick Thistle and Aberdeen face sanctions over matters at the end of the season, with the direct incidents not listed by the SPFL.
The league body saluted "incredible support" in Scotland, with attendances up to a record high in the SPFL era. Numbers jumped by 185,000 on the previous record last year to 5,336,353 supporters.
However, unsavoury incidents prompted condemnation from the SPFL with "dangerous, irresponsible and selfish behaviour" blasted by chiefs.
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An SPFL statement read: "While the vast and overwhelming majority of supporters are an undoubted force for good in our game, it’s been extremely disappointing to see a small number persisting with dangerous, irresponsible and selfish behaviour. Whether that’s flares, fireworks, smoke bombs, throwing missiles, or pitch invasions, these actions put staff, supporters and players at risk and are completely unacceptable.
"For example, the incident which saw Aberdeen player Jack Mackenzie left injured at Tannadice Park after a chair was thrown onto the pitch, simply beggars belief. It goes without saying that players, staff and fellow supporters should have the right to attend games free from the risk of being struck by projectiles.
"The swift cooperation between clubs, supporters and Police Scotland helped identify the alleged perpetrator, who has since appeared in court. This is a model of how our system should work. In another recent incident, Livingston quickly issued a lifetime ban to an individual who allegedly spat at a member of the Ross County coaching team, and we commend the club’s prompt and decisive action.
"As well as club bans, unwelcome incidents such as these have unfortunately made it abundantly clear that there is a need for far more widespread use of football banning orders (FBOs) and we are encouraged by the progress being made in partnership with our clubs, Police Scotland and the Scottish Government.
"We have been discussing broadening the scope of these orders as part of the Scottish Government’s FBO working group and we’re extremely pleased to see this was covered in the Programme for Government in May. These recent incidents reinforce the need for such sanctions to protect the match-day experience for the vast majority of law-abiding fans.
"During the 2024/25 season the SPFL took disciplinary action against a number of clubs and notices of complaints have now been raised against three clubs in respects of incidents which occurred at the end of the season - Partick Thistle, Aberdeen and Celtic.
"The SPFL will undertake a number of discussions with supporter groups to better understand their views and explore the challenges involved. We’re committed to open and constructive engagement as we work together to ensure a safe, enjoyable and inclusive match day experience for all fans.
"We will be having further meetings with key stakeholders over the summer to review the most recent season and look ahead to 2025/26. We remain committed to ensuring a safe and enjoyable match day experience for players and supporters - they are the lifeblood of our game and deserve nothing less."
