Cologne were charged with four offences at the match which was delayed by an hour after large numbers of their fans descended on the Emirates Stadium in north London, the majority of them without tickets.
Many bought tickets for areas of the stadium occupied by Arsenal supporters, causing segregation issues, although there were only isolated incidents of trouble once the game started.
Arsenal, who face one charge of a breach of safety and security regulations, said they had worked with the Metropolitan Police and UEFA in deciding whether the game, which the English team won 3-1, went ahead.
"Following last night's match we would like to stress that fan safety was always our paramount concern and informed all decisions made," Arsenal said in a statement.
"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 kickoff.
"Many tickets were sold through touts and this is very disappointing," the club added.
"We worked in full consultation with police and UEFA officials on the night and in advance of the game and had taken extensive steps in advance to prevent tickets being sold to visiting supporters."
UEFA said Cologne had been charged with crowd disturbances, the setting off of fireworks, throwing objects and acts of damage to the stadium. Arsenal were charged over the blocking of a stairway in the away end.
Arsenal have launched a full review into the circumstances surrounding the game while the Police said they would work with the club and UEFA to establish how away fans were able to access the home supporters' seating.
Arsenal denied claims that some Cologne fans had acquired tickets by joining Arsenal's membership scheme.
"No red memberships purchased after the draw were able to be used to get tickets in the home end for this match," Arsenal said. "We also worked with our colleagues at Cologne to stop supporters travelling without match tickets."
Bundesliga club Cologne were playing in Europe for the first time for 25 years and an estimated 20,000 of their fans marched through the streets of London earlier in the day.
Police said five people had been arrested, all on suspicion of public order offences, and three officers had been injured, none of them seriously.
UEFA's Ethics and Disciplinary Body will deal with the case next Thursday.
