Hughes felt Arsenal's goal was offside.
He said: "I have seen the replay, Arteta is offside twice, on the initial header that Julio saves and in the melee he comes back from an offside position and scored.
"How the referee hasn't given offside, I don't know.
"We have gone in and asked for an explanation and he has come up with some explanation about Ryan Nelsen leaving the field of play so that played everybody onside.
"I have no idea what he is going on about, but that's what you're up against."