Gunners boss Wenger, who stripped William Gallas of the captaincy at Eastlands, claimed the scoreline "flattered" City.
Hughes told the BBC: "Maybe he is being a little bit ungracious because I remember Robinho going around (Manuel) Almunia to make it even more emphatic.
"We had another couple of good opportunities, so I do not think the scoreline flattered us at all. We created six or seven chances."
Gallas did not travel with the squad after making critical remarks about the team in midweek when he questioned their fighting spirit.
While Wenger confirmed the French defender still had a future at the club he refused to discuss the reasons behind his absence.
"I will not speak about William Gallas in a post-match interview, " said Wenger. He is a player who did not play today, so what can he do? Nothing.

