The Group H opener, in which Arsenal ran out as 3-1 winners, was delayed by an hour as ticketless Cologne fans looked to gain entry to the ground.
The visitors were issued with 3,000 tickets, but around 20,000 Cologne supporters are believed to have made the journey to London.
There were clearly thousands of away supporters sitting among Arsenal fans, causing a security risk, and five arrests were made over the course of the evening.
Arsenal issued a statement this morning insisting the safety of supporters was the main concern at the time as the Premier League club “launched a full review” of the events.
And both clubs now face disciplinary charges from governing body UEFA.
Cologne’s charges include crowd disturbances, setting off fireworks and acts of damage.
While Arsenal face a probe after blocking stairways in the away end of the Emirates Stadium.
UEFA will deal with the case on September 21, the governing body have confirmed in a statement.
Speaking after the game Wenger expressed his disappointment at the night’s events.
“I’ve followed German football for a long time and I thought Cologne had not played in Europe for 25 years,” Wenger said.
“On the first night they go out [to play], they spoil their night.
“I couldn’t understand that. Were the problems created by people who had no tickets? I don’t know.
“But certainly they had more people here than tickets so that was certainly the cause.
“We left that to the police – I’m not better informed than you. I just had to speculate on if the game was not played, what would we do.”
When asked if UEFA should take action, he added: “They are the only master to analyse the facts, what happened. They will certainly make an inquiry to see what happened, for sure.”
Arsene Wenger also admitted at one stage prior to the first whistle blowing that the game would have been postponed with the police deeming it unsafe.
“We waited patiently in our dressing room but what was difficult was for me was I had all kind of plans to think about at some stage,” Wenger said.
“I had to think if we play tomorrow at what time do we want to play, do we play next week… but they have the Bundesliga again in midweek, and we had a League Cup game midweek as well.
“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.
“But in the end at some stage I thought they would not play the game, because I can’t see the police taking any risk.
“We live in a society of 100 per cent security and I thought they would never take a gamble to play this game when I saw the images around the stadium.
“But I must say our supporters as well dealt well with the situation as well and there was no aggravation. I hope everything goes well after the game.”