The Arsenal boss was sent from the dug-out in stoppage time after kicking a water bottle in frustration when Robin van Persie had an equaliser ruled out after William Gallas had strayed offside.
Arsenal were also denied a penalty in the first half when Darren Fletcher clattered into Andrey Arshavin, while United drew level from the spot after Manuel Almunia brought down Rooney.
Explaining why he was sent off by Dean, Wenger also questioned why an unnamed United player did not get booked during the game.
"Because I kicked a bottle when the goal was cancelled from an offside position," Wenger told Sky Sports when asked about his dismissal. "I didn't know we were not allowed not to do that.
"You know what you get at Old Trafford when you come - every time - but I do not want to go into the performance of the referee. Any questions you should ask him."
Emmanuel Eboue was booked for diving in the second half, but when asked about the decision Wenger commented: "I believe you should look at the game and who played with real spirit on the pitch today. I felt we played with the right spirit
"It's difficult to judge every time someone goes down. Today I've seen a player make 20 fouls and there was no yellow card. Nobody sees it."
Asked to elaborate on the identity of the player, Wenger added: "If you've seen the game you don't need me (to tell you). How this player got away without a yellow card is quite amazing."
Arshavin had given the Gunners a first-half lead before Rooney levelled from the spot and Abou Diaby's own goal gifted United the points.
The defeat ended Arsenal's 100 per cent start to the season, but Wenger drew encouragement from his side's performance.
He said: "We go home with no points and that is very frustrating. When you play like that to go home with no points is very difficult to accept.
"But I'm very positive because we showed great quality. Our performance is very encouraging for the future and there are more positives than negatives from today's game."
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