Jon Moss sent off the away side's Steven Pienaar and denied the hosts a late penalty kick in a "frustrating" performance at Loftus Road.
The visitors were reduced to 10 men when Steven Pienaar received his marching orders for two fouls in the space of 10 second-half minutes, before Moss chose not to award QPR a "stonewall" penalty following Seamus Coleman's clumsy trip of Junior Hoilett.
Hoilett had given bottom-of-the-table QPR the lead after just four minutes before Julio Cesar contrived to turn Sylvain Distin's header over his own goal line after it rebounded back off the post, leaving the two sides level at the break. By the hour mark, Moyes' side was a man light as Pienaar saw red for a foul on Jose Bosingwa.
"It was very, very harsh to give somebody a red card for that, incredible," Moyes told reporters after the match. "We actually watched a clip last week on Jelavic, very similar – we didn't get a penalty for it against Wigan two weeks ago – this one, I don't know if he even clipped the boy. I think he hit Steven's rather than Steven clipping him so I think it was the wrong decision, definitely."
With fourth-placed Everton on the ropes, QPR pressed for a winning goal and in the midst of a sustained period of pressure, Hoilett tumbled under the challenge of Coleman.
The decision not to award a spot kick incensed Hughes, who complained in the post-match press conference, "In the end, we should have had a stonewall penalty anyway, the referee was only four meter away so why he hasn't given it, I have no idea. But in fairness, he frustrated both teams and both sets of supporters today. ... Not one of his better games."
The Loftus Road outfit remain anchored to the bottom of the Premier League after failing to claim a win in eight attempts, but Hughes remained buoyant following a performance full of positives.
"We've gone up against a team that has started the season like a house on fire and more than matched them and on another day should have beaten them," Hughes said. "We're pleased with the level of performance in the first half, albeit we've let ourselves down on a set-play where we need to do a lot better than we did and take responsibility to stay with your man. You shouldn't allow a big powerful center half have a free header from six yards. That shouldn't happen."