The Gunners let a two-goal lead slip against their German hosts, allowing Schalke to claim a point following a dominant second-half display.
Wenger believes that match official Nicola Rizzoli made a mistake in the build-up to Schalke's first goal and stopped play incorrectly with Arsenal in an advanced position in the second half.
He told reporters: "Yes, [it was a foul] on Theo Walcott and he gave the foul against him. I invite you to see it again. It is a foul from Ibrahim Afellay on Walcott, 100%.
"I must say there was another decision that was absolutely amazing.
"It was the first time I saw that in my long experience, to stop the game when a player has rolled over on his ankle. I have never seen that when you have a goal chance."
A draw in Germany means Arsenal remain second in Group B, a point behind Schalke and one ahead of Olympiakos in the fight for Champions League qualification.