Celtic were incensed and UEFA handed Eduardo a two-match ban for diving.
Arsenal protested and had the suspension lifted on appeal, but Wenger now feels there could be a backlash.
"I fear completely that we may not get the penalties we should after Eduardo.
"Some referees may go into the game with what happened in their mind.
"What happened with Vela was unbelievable. I hope what happened with Eduardo is not an influence but it did come into my mind after the game. Eduardo was a big case."