For the second time in 24 hours, a side mired in relegation trouble were the victims of a shocking decision as United's march to the title continued.
QPR's hopes of capitalising on Wigan's misfortune on Saturday were virtually ended after 13 minutes when skipper Shaun Derry was sent off for fouling Ashley Young inside the box.
Contact was minimal to start with, that Young was clearly offside when he received Wayne Rooney's through ball just made the call from referee Lee Mason even more farcical.
United should have run up a huge score, such was their overwhelming dominance thereafter.
Instead, they were forced to rely on a second-half piledriver from Paul Scholes to wrap up a win that keeps them on course to clinch a 20th championship.
Their day was made even better after seeing Arsenal sink title rivals Manchester City 1-0 at The Emirates, where Mikel Arteta scored a late winner and Mario Balotelli saw red in stoppage time.
Yet the recriminations from the Old Trafford blunder will last for some time.
Indeed, after this weekend's events, some bosses would argue what should be a thrilling fight to avoid relegation is in danger of being decided by who ends up with the most incompetent officials. That so much in prestige and finance is being risked seems frankly wrong.
The two abysmal decisions that condemned Wigan to defeat at Chelsea were matched by the appalling conclusion reached when Rooney slid his pass through to Young.
The linesman was in exactly the right position too, making his judgement even more mystifying.
Hughes strode the touchline in utter disbelief just as Roberto Martinez had done at Stamford Bridge 24 hours earlier.
Club officials protested vehemently on Twitter, with chief executive Phil Beard likening Young to British Olympic diving hopeful Tom Daley and owner Tony Fernandes declaring simply: "Awful. Spoilt another game". Fernandes also wrote that the club intended to appeal Derry's red card.
Rooney did not care of course, ramming home the spot-kick for his 29th goal of the season.
Behind, down in numbers and without Joey Barton, who is one booking away from a two-match ban, and Bobby Zamora, left on the bench after a recent head cold, QPR found themselves in an impossible situation.
United effectively set up camp around the visitors' penalty area and the only wonder was they had not increased their advantage by half-time.
Rooney brought a couple of decent saves out of Paddy Kenny, first with a curling free-kick, then a chip that was bound for the top corner.
Antonio Valencia was furious that a far more plausible penalty appeal than the one that had been given was turned down after he had been bundled over by Taye Taiwo.
Patrice Evra lashed a shot wide and Danny Welbeck had an effort charged down by Anton Ferdinand as QPR mounted a brave rearguard action.
Selected ahead of Javier Hernandez, Welbeck was eager to do well but was denied a goal at the start of the second half by an offside decision that was far closer than the earlier one.
Welbeck then fired well over from an acute angle, much to the frustration of Sir Alex Ferguson.
As with their previous home game against Fulham, United were failing to make their pressure tell.
Rooney was the next to waste an opportunity, although it was a half-chance, and Kenny needed to make a save.
Rafael should have scored after being brilliantly picked out by Scholes but the young Brazilian panicked, driving his shot straight at Kenny, who had gone down early, the ball then rising up onto the crossbar and bouncing to safety.
Welbeck was set up by Rooney and despite having two goes, failed to beat Kenny, who repelled the initial shot, then gathered the follow-up as it was stabbed goalwards.
It needed an old head to take control and Scholes duly obliged, drilling home from 25 yards after Abel Taarabt had gifted possession to Rafael.
Michael Carrick's ferocious 35-yard shot came crashing back off a post as United tried to improve their goal difference, which Ferguson continues to insist might be significant.
The return of DJ Campbell after three months out with a hamstring injury, could be just as notable for QPR, although that is of small comfort for Hughes, who just like Martinez, stormed away shaking his head at the injustice of it all.