Referee Graham Poll endured the wrath of the Division One side for his role in the build-up to Freddie Ljungberg's strike.
Wayne Allison went down under a challenge from Sol Campbell but Poll decided not to blow the whistle.
Instead Arsenal broke at speed with Poll compounding United's grievances by colliding with Michael Tonge to prevent him from intercepting a pass which led ultimately to Arsenal's goal.
The Gunners took full advantage through Ljungberg and, thanks to David Seaman's enduring reflexes with six minutes left to pull off an almost unbelievable save - and yet more good fortune, they eventually prevailed.
It was not until the 35th minute that the game exploded into action, let alone controversy.
With Allison still lying on the ground after being unceremoniously tackled from behind by Campbell, Arsenal finally managed to break with their normal pace and poise.
With first Allison and then Tonge out of the picture, Francis Jeffers was allowed space to scuffle his way to the byline.
His low cross was scuffed against the far post by Wiltord, who chased the loose ball and saw his next effort blocked. However, the ball rebounded only as far as Ljungberg, who was lurking on the penalty spot and drove his shot high into the net.
The real credit, however, went to Seaman, who somehow clawed the ball off the line after substitute Paul Peschisolido had flicked on Carl Asaba's shot with his head.
That was the one moment of true class on a heated afternoon when United gave Arsenal a real run for their money but lacked the finishing or fortune to make it through.