The German club face four charges, including crowd disturbances and setting off fireworks, while Arsenal face a charge over blocked stairways.
Thursday’s match was delayed by an hour as thousands of Cologne fans arrived at Emirates Stadium without tickets.
Koln said “the security concept and communication seemed inadequate and the police force too small”.
About 20,000 Cologne fans arrived in London for the first match in the group stage despite a ticket allocation of only 2,900.
This case will be dealt with by the Uefa’s control, ethics and disciplinary body on 21 September.
Koln ne said they were “proud that tens of thousands of Colognians wanted to experience the first European match in 25 years and made their way to London”.
They added that the “overwhelming majority” of fans who travelled represented the club, the city and German football “happily and positively”.
A 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.”
Koln distanced themselves from “so-called disturbers” who “threatened, insulted, and even attacked stewards and police officers without cause”, saying there was “no excuse or justification” for their actions.
On the situation before the match, the statement added: “Despite the tremendous experience of both the London security forces and Arsenal as a permanent partaker in European football, the organisers were unfortunately not adequately prepared for the task.”
Arsenal have started a review and their statement on Friday read: “We worked with our colleagues at Cologne to stop supporters travelling without match tickets.
“The 3,000 tickets issued to Cologne fans was in line with competition rules but it is clear many more visiting fans arrived, causing significant congestion and disturbance outside the stadium before kick-off. Many tickets were sold through touts and this is very disappointing.”
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