Wenger's troops looked on course to bounce back from their 6-0 thrashing at the hands of Chelsea at the weekend, as a quick-fire double from Lukas Podolski and Olivier Giroud put the Gunners minutes from victory.
However, Flamini diverted the ball into his own net in the dying stages of the contest, and Wenger says that the concession was borne out of being "too conservative" as a result of Saturday's demolition in West London.
He told reporters: "It's difficult to swallow because the team gave absolutely everything tonight, their spirit was great. You wonder how we could draw a game like that, they had nothing and in the end it was 2-2.
"Basically, we gave them the two goals but overall the spirit was great and we have to recover from that last goal.
"The spirit was absolutely brilliant and you have to give credit to the players, even if result didn't go our way. At 2-1 we became too conservative because of what happened on Saturday and instead of continuing to attack it worries us more to keep the score."
The North Londoners host Manchester City at the weekend.