The Gunners were leading thanks to Tomas Rosicky’s 38th-minute opener but were pegged back in the 65th minute through Giannis Maniatis, before substitute Kostas Mitroglou secured the win for the Greek side.
Wenger felt referee Alberto Undiano Mallenco incorrectly pointed for a corner after a Paulo Machado header looked to have hit the post and went behind in the build-up to the home side’s equaliser.
“For their first goal, it was a goal kick, simple as that,” Wenger told ITV1. “What is the fifth referee doing behind the line? Nobody knows. I don’t think it was the right decision, but we have to cope with it. After that they scored a good goal.”
Wenger’s side missed the opportunity to top their group after Schakle’s 1-1 draw at Montpellier and marked the north Londoners’ second straight defeat after Saturday’s loss to Swansea City.
“We have to wait for the draw but ideally you want to finish first,” Wenger continued.
He added: “It was an interesting game. We had a good first half but dropped physically in the second.
“Many of the players are not used to that level. We had two or three chances to score a second but after that we know we can be in trouble. We needed the second goal tonight.”
Wenger said: “It’s a key question that I cannot answer directly after a game like tonight. What is important is that we do well until January.
“We have big games coming up and we should focus on the players we have to win the games.”