Kickoff was delayed by an hour after an estimated 20,000 visiting supporters, many of whom were ticketless, descended on North London.
UEFA has since charged Arsenal with blocking stairways in the away supporters section of the stadium during the Group H fixture.
Koln, meanwhile, face four counts - crowd disturbances, the setting off of fireworks, throwing objects, and acts of damage.
While the German club have condemned the acts of those fans who fought with police and Arsenal fans, they criticised how the event was handled.
The statement read: "1. FC Köln is proud that tens of thousands of Colognians wanted to experience the first European FC match in 25 years and made their way to London. The overwhelming majority of our fans have represented the club, the city of Cologne, and German football happily and positively. The London locals and the police shared these feelings on social media leading up to the match.
"Due to the enormous demand for tickets, it would have been sensible, not least for security reasons, to allow more than the allocated 5% of stadium capacity to the guest fans. It was apparent that thousands of people from Cologne would seek to avoid the restrictions and get tickets in every way possible. One such way would be through the help of Arsenal supporters, who passed on their tickets to the FC fans. Some as gifts, but some also for horrendous prices. Arsenal FC has described the extent of this second ticket market as "disappointing" and has announced that further clarifications of the circumstances will be evaluated.
"Despite 1. FC Köln and Arsenal FC urging fans to purchase tickets only through official channels and not to enter any sections other than the guest section wearing FC merchandise, the situation before the match showed FC fans lining up in various sections to enter the stadium. And also despite the tremendous experience of both the London security forces and Arsenal as a permanent partaker in European football, the organizers were unfortunately not adequately prepared for the task. In our view, the security concept and communication seemed inadequate and the police force too small.
"The most important common goal of having the match played on the same evening was achieved by allowing fans with valid tickets to quickly take their seats. This procedure proved to be the correct decision. Finally, the course of the match showed that the mixing of home and away fans did not constitute a safety risk for this match.
"1. FC Köln will intensively evaluate and work together with Arsenal FC, the security forces, and the representatives of UEFA to discuss what measures need to be taken to prevent such things, such as the shifted kick off time, in the future.
"That said, 1. FC Köln would like to unmistakably make it clear that there is no excuse or justification for the fact that a group of so-called disturbers threatened, insulted, and even attacked stewards and police officers without cause. We distance ourselves from this explicitly. These people are solely responsible for the fact that a football match with a special meaning for an entire region, as well as the courageous effort of our team on the pitch, had to be overshadowed by scenes that had nothing to do with sport and fair play. Although 1. FC Köln is not responsible for the acts of these so-called disturbers, we ask our English hosts to accept our apology."
Arsenal, who won the game 3-1, announced that they will be undertaking a full review into the events on Thursday, and added that "the safety of everyone in and around Emirates Stadium is always our paramount consideration".