QPR were set up to secure a draw against the north London side and Hughes’ strategy appeared to be working with game goalless after 75 minutes.
However, Stéphane Mbia’s red card prompted a response from the Gunners, with Arteta scrambling the ball into Júlio César’s net in the 82nd minute to seal victory.
“The referee has absolutely killed it to allow their winning goal because Arteta was clearly offside on two occasions,” Hughes said.
“I’ve been to see the referee in his dressing room and he has created some cock and bull story about Ryan Nelsen being off the pitch.
“I’ve no idea what he is going on about because Ryan Nelsen, at no stage, went off the field of play. It has cost us the point.”
Hughes’ men looked resolute for the majority of the match, with Arsenal struggling to break down a much-improved QPR rearguard.
However, Mbia was shown a straight red after kicking out at Thomas Vermaelen following a foul on the Cameroon defender by the Gunners captain.
The QPR manager admitted his frustration at seeing the former Marseille man needlessly sent off when the referee had awarded the visitors a free-kick.
“He’s obviously very upset,” added Hughes, whose side remain rooted to the foot of the table. “The frustration from our point of was the foul had been given our way.”
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