Arsene Wenger questioned the officials after a controversial call that led to Olympiakos' equaliser as Arsenal crashed to a 2-1 defeat in Greece.
Tomas Rosicky had given Arsenal a first-half lead with a fine finish after Gervinho's cut-back, but a youthful Arsenal side could not hold on to their advantage as their hopes of finishing top of Group B evaporated.
Olympiakos were wrongly awarded a corner after the referee decided Wojciech Szczesny had turned an effort round the upright, when it actually clipped the post. From the corner, Giannis Maniatis brought Olympiakos level, and the hosts went on to win as Kostas Mitroglou fired home.
"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."
Had Arsenal won, they would have topped the group as Schalke were held to a 1-1 draw at Montpellier. They also missed the chance to restore some momentum after Saturday's demoralising home defeat to Swansea.
"We have to wait for the draw but ideally you want to finish first," Wenger 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 refused to discuss any potential January transfer targets, as fans clamour for big signings with Arsenal having won just one of their last six matches.
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."