The game was delayed by more than an hour as thousands of away fans arrived at Emirates Stadium without tickets.
About 20,000 Cologne fans turned up in London despite the German club being given a ticket allocation of 2,900.
This case will be dealt with by the Uefa Control, Ethics and Disciplinary Body on 21 September.
Arsenal have launched 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."
Arsenal manager Arsene Wenger said he was surprised the match - which his side won 3-1 - was played.
"Do we move it to Tuesday and play Thursday? It was all kind of speculations you know that we had to analyse and see how we can deal with the situation," he said.
Cologne coach Peter Stoger refused to be questioned on the actions of his club's supporters: "I have no comment about the fans," he said.
"I'm the coach, my job is the team, my job is football, not the fans."
Police said five people had been arrested on suspicion of public order offences.