Thousands of ticketless Cologne supporters turned up at the Emirates Stadium and those fans with tickets were unable to gain access to the ground.
Away supporters could also be seen celebrating Jhon Cordoba's ninth-minute strike in pockets among home fans around the ground.
The case will be dealt by the UEFA Control, Ethics and Disciplinary Body on 21 September but Arsenal issued a full statement explaining their version of events.
Speaking after the match Arsene Wenger said: 'They (Cologne fans) were very clever.
"It's hard to say, it was similar for Cologne".
"We had a slow start and there was accidental goal".
'They are a big rival, if you see their squad they have a lot of top players, said Conte.
Wenger said: "You have to live with all kinds of opinions, but at the end of the day you have to make decisions, rational decisions, and these decisions are guided first by the sportive interests, but as well by the financial respect of your balance sheet. I don't know how they managed to infiltrate our fans and get everywhere but they did that very well", he said.
Arsenal's Europa League game against FC Koln descended into chaos and violence as 20,000 German fans travelled to North London - far above the club's 3,000 ticket allocation.
Once the game began, however.
Cologne manager Peter Stoger refused to comment on the crowd issues at the Emirates, saying "my job is to talk about football not fans".
"We want to do well in all the best competitions and I had an experienced team today, even though I made nine changes". This included Chelsea's 6-0 humbling of Azerbaijani club Qarabag in the midweek Champions League tie.