An estimated 20,000 fans made the trip to London for Cologne's first European fixture in 20 years, although their ticket allocation at the 60,000-capacity Emirates Stadium was a mere 3,000.
A vast number of those travelling fans found their way into home sections of the stadium, with the confusion causing kick-off to be delayed by an hour. Arsenal won the game 3-1, the contest passing with relatively little trouble.
Regardless, Cologne have condemned the actions of some supporters, who had tried to fight their way into the away end past stewards, while also questioning why their fans were not afforded a bigger allocation.
A club statement read: "Due to the enormous demand for tickets, it would have been sensible, not least for security reasons, to allow more than the allocated five per cent 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 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.
"That said, 1. FC Koln 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 Koln is not responsible for the acts of these so-called disturbers, we ask our English hosts to accept our apology."
Arsenal vowed to bar any of their supporters found to have passed on tickets to Cologne fans, adding: "We would like to take this opportunity to thank our supporters for their patience and conduct during what was a very difficult night for us all.
"We know that many supporters experienced significant disruption getting to the match and also inside the stadium during the match. We thank everyone for their understanding."