Lyon could be banned from all European competitions by UEFA after at least eight police officers were injured in scuffles with home fans before their game against CSKA Moscow in France.
The Ligue 1 club still have a ban, suspended for two years from April 2017, hanging over them after their fans caused trouble in last season's Europa League quarterfinal.
The UEFA Control, Ethics and Disciplinary Body (CEDB) has announced that another disciplinary proceeding has been opened after their aggregate win against the Russian club.
Three arrests were made, RMC reported, after at least 100 people attacked a specialised police unit, hurling missiles and seriously damaging their vehicle before riot police arrived to break up the group.
UEFA has charged Lyon with racist behaviour, crowd disturbances, setting off fireworks and blocking stairways, and announced the case will be dealt with on May 31.
Meanwhile, three Marseille fans were detained by police and two security guards were taken to hospital, one after being stabbed in the neck by a sharp object.
The game, which Marseille won to advance to the quarterfinals on aggregate, was considered "high risk" by local authorities. A total of 800 officers, including 200 from a private security firm hired by Athletic, were placed on duty.
However, Marseille supporters still managed to take flares into the stadium, light them and throw them towards the home fans during the game, prompting UEFA to charge the French club for crowd disturbance and use of fireworks.
"Deplorable attitude by some 'fans' of Marseille," Bilbao mayor Juan Mari Aburto wrote on Twitter. "I reiterate my revulsion over these undesirable ones that hide in football to bring out their true violent, ultra and unsportsmanlike face. I wish a prompt recovery to the two Athletic security guards."
The case will be dealt with by CEBD on March 22.