Thousands of visiting fans gained access to the home end and made their presence felt throughout the encounter, with estimates suggesting that 20,000 German fans travelled to London without tickets for the encounter.
Many found their way into the home end of the ground, where they created a boisterous atmosphere, yet UEFA has taken a dim view of the way the fans were controlled by the Gunners and by their own club.
European football's governing body has announced that Arsenal face a charge of stairways being blocked in the away supporter sector.
Cologne, meanwhile, have several more charges to face, including crowd disturbances, setting off of fireworks, throwing of objects and acts of damage.
UEFA has confirmed that a hearing date of September 21 has been set.
Arsenal, meanwhile, have confirmed that they have launched their own investigation into what happened on the evening.