With qualification already secure ahead of the last Group B tie, Wenger had elected to leave several first-team regulars behind as 20-year-old defender Jernade Meade made his European debut.
Wenger, though, is not overly concerned. He said: "We need a good Christmas present now (in the draw), but we will see. We can get a bad draw or less strong team, but you normally get strong teams through anyway now."
Although Tomas Rosicky fired the English side ahead on 38 minutes, the Greeks fought back through a somewhat controversial effort by Giannis Maniatis and a well-taken strike from substitute Kostas Mitroglou to leave Wenger facing more questions about his team - who have now not won in the last four and plummeted down the Premier League table.
Defeat in the Georgios Karaiskakis Stadium for a second successive season coupled with Schalke's draw in Montpellier means Arsenal will head into the knockout stages without the security of a top seeding.
But Wenger said: "The disadvantage we have is we play the second game away, but that is not statistically proven to be a such a disadvantage. Let's see, but for now it is important for us to focus on the [domestic] championship, forget about the Champions League a little bit and get ourselves back in decent form in the championship."
Wenger tried to remain upbeat despite the disappointing final outcome in Athens, and he said: "We left eight or nine players at home and we had a positive game.
"We had a good first half, but we dropped physically in the second half because many players lack competition at that level and therefore we couldn't take the chances for the second goal.
"We also got a very bad decision against us on the (first) goal. I am not against the fifth referee, but you would like at least for them to be concentrated on their job, but that was not the case, Wojciech Szczesny was far away from the ball.
"Why didn't the fifth official tell the referee? It's difficult to understand, to concede a corner when it doesn't go off the goalkeeper. However, I don't want to make a fuss of it, so we have to take it on the chin and go home and focus on our next game."