Gunners goalkeeper Wojciech Szczesny was shown the red card when he went for an attempted "through ball," but was a step late, colliding with incoming attacker Arjen Robben in the process.
The French manager pointed out, after the game, that there was no intention from his shot-stopper to impede the Bayern player's path, but rather, Robben, did very well to sell the call, and so did the entire Die Roten squad to their advantage.
"He has enough experience to know to make more of it," Wenger told arsenal.com.
"Overall I thought Bayern made a lot of every single contact, we are not used to that in England."
"There were fouls given today that usually are not given in the Premier League, but it's different rules and we have to accept it."
Wenger believes that it was a turning point that led to a one-sided ball game.
"Unfortunately it changed the game completely and didn't just change the game but killed the game," he added.
"The game was, until then, top quality, and in the second half it was boring for neutral people. It was one-way traffic. The referee made the decision that killed the game."
Nevertheless, he still believes that his squad can make something out of the second leg when they visit the Bundesliga outfit at the Allianz Arena in March.
"It isn't over because we will fight until the end. We knew at half-time we had to try and keep it at 0-0 and we will see what happens," he disclosed.