Dinamo Zagreb midfielder Arijan Ademi was banned from football for four years after he was found positive for a banned substance following his club's victory over the Gunners in Champions League in September.
When asked if he finds it strange that UEFA have let the result of that particular match stand, Wenger said: "Yes, of course.
"It's a surprising rule. UEFA applies the rule that is planned but I personally don't agree with the rule. You cannot say that they had a doped player but the result stands.
"That means you basically accept doping. But it is the rule and we accept that. We have to look at ourselves and deal with our own performance."
But Wenger also concedes that he doubts whether his opinions will receive the public backing.
"I don't know if I would have the support of anybody but I came out on that and as a result we had a doping control from UEFA on Friday," he added.
"We had 10 people on Friday to control us. I do not want to speculate too much on the career of a player. In between (the match in September and now) he has been punished. There are two things: our performance on the day and the fact that they had a doped player."