The Rs boss has claimed that Gunners midfielder Mikel Arteta was offside as he poked the ball home to hands the hosts victory in the 84th minute on Saturday afternoon
The Spaniard poked the ball home with six minutes of normal time remaining to seal a 1-0 victory for the Gunners and deny the 10-man Rs a share of the spoils.
And, despite admitting that Stephane Mbia's red card was perhaps deserved, Hughes took issue with the late goal which won the game.
"The sending off changed the make-up of the game," the 48-year-old told reporters.
"Unfortunately we’ve conceded a goal during that period which, when the referee sees it again he’ll understand he’s made a huge mistake. The lad is clearly offside on two occasions leading to the goal.
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"We’ve been in to see the referee and he’s conjured up some story about Ryan Nelsen because he left the field of play he played everybody onside.
"I have no idea what he’s going on about because Nelsen didn’t at any stage leave the field of play."
The Welshman went on to condemn Thomas Vermaelen's reaction to contact from Mbia but conceded the midfielder's actions were ill-advised.
"There's very minimal contact but Vermaelen is going to make the most of that situation. He dives and rolls around and makes sure the referee makes a decision.
"Obviously there's contact, it's a wild challenge and it's a sending off but unfortunately that really hurt us."