Wenger felt City's Raheem Sterling dived for the penalty that gave the hosts their second goal and that the third should have been ruled offside.
"I feel the referees don't work enough," Wenger said.
"The level drops every season at the moment and, overall, it's unacceptable."
With the scoreline at 1-0, referee Michael Oliver awarded City a penalty after Sterling went down under a challenge from Arsenal's Nacho Monreal.
Sergio Aguero converted and, after Alexandre Lacazette pulled one back for the Gunners, Gabriel Jesus poked in City's third when both he and David Silva could have been flagged for offside.
"I believe it was no penalty," Wenger told BBC Sport. "We know that Raheem Sterling dives well, he does that very well.
"The third goal was offside. I am very upset because at 2-1 we were in the game.
"The third goal was the killer and it is by coincidence that mistakes always go for the home team, as we know. You can accept it if City win in a normal way, but this is unacceptable."
The win gave City a ninth successive league victory, a club record for a single season.
Manager Pep Guardiola declined to discuss the decisions that went for his side.
"We won in the best way," the Spaniard said. "Sometimes it's like this.
"I was told it was offside and I don't want to win like this, but earlier this season Arsenal beat Burnley with a handball in the 96th minute." PLACE YOUR TEXT ADVERT BELOW:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> How I Made Me =N=2.5 MILLION In 7 Days from 2 Common Product I Imported and how you can do the same. Click HERE FOR FREE Details right now Warning To Men: This 3 Foods Is Killing Your Erection. Click Here To Know Them