Wenger, who was criticised by Everton manager Ronald Koeman for airing gripes about officials earlier in the week, felt offsides were missed in the moves for both City's goals at the Etihad Stadium.
Replays suggested Leroy Sane may have been marginally offside as he cancelled out Theo Walcott's opener, and Wenger also raised question marks over the positioning of David Silva as Raheem Sterling struck the winner.
Wenger said: "We conceded two offside goals which is very difficult to accept in a game of that stature but, as it is well known, the referees are protected very well like the lions in the zoo, so we have to live with those decisions."
Asked for clarification on his remarks, Wenger said: "I want them to be very well protected, I want them to be safe, but if they could make the right decisions it would be even better.
"But it is too long a subject
I do not want to make referees the subject of the press conference."
Gunners goalkeeper Petr Cech, who was beaten at his near post as Sterling cut inside from the right to strike winner, was also unhappy about the winning goal.
Cech told Sky Sports: "There were players in front of the goal so I didn't see the shot and there were people running across
I don't know if one of them was David Silva or not but, as I said, I didn't see the ball because it was behind the players."
Wenger did bemoan his players' performance as well, with the defeat coming after a similar reverse at Goodison Park.
The Frenchman said: "I felt we were in control and it didn't look like we could lose the game
We stopped them from creating chances and they looked a bit short of ideas to create chances.
"But we were caught cold in the second half and we dropped physically
Maybe we dropped a bit mentally when they equalised.
"They killed the game well, they have experience
They slowed it down and it was difficult to create the flow."
Wenger confirmed that Alex Oxlade-Chamberlain, who came on in the second half only to be taken off again 13 minutes later, had suffered a "muscular injury".
City also replaced the hard-working Pablo Zabaleta at half-time, with it later emerging the right-back had suffered a knee injury he hopes is not too serious.
For City, the victory was only their second at home in three months in the league
They seemed lethargic in the first half but showed greater intensity after the break to claim a victory that lifted them to second in the table.
Manager Pep Guardiola said: "Of course it means a lot to win against one of the best teams in the Premier League, Arsenal
It was a good comeback.
"We were unlucky in the first minutes when they scored the first goal
They were lucky.
"It was a good game
I think we dominate, like what we are looking for
The victories give a lot of confidence in the mind of the players in what we are trying to do.
"I am so happy for the fans
They stayed until the 94th minute
Normally, in the last games, they have gone with 10 minutes left
We have to play good and they are going to stay with us."
The match was the second in succession in which Guardiola left £50million centre-back John Stones on the bench.
Guardiola said: "I just apologised to John because he didn't deserve to be left out
I love him a lot but I just tried to keep the same back four we played against Watford."
Source : PA
Source: PA