The Red Devils were denied an opener earlier this month after a review lasting nearly four minutes at Craven Cottage.
A free-kick was squared by Alejandro Garnacho to Scott McTominay, both onside, and the on-field decision was goal.
However, Harry Maguire was deemed to be interfering with play from an offside position.
The United defender did not touch the ball but made an attempt to play it - and VAR referred referee John Brooks to the screen for a subjective offside call.
VAR audio of the incident was released on Tuesday night - and United fans were not convinced by the process.
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One fan wrote on X, formerly known as Twitter: "Anything subjective should mean that VAR can't change with the on field decision. They're literally saying Maguire's attempt and block was subjective, so how could they then overturn based on subjectivity?"
Another said: "The VAR audio from McTominay's disallowed goal vs Fulham just seems to show lots of people getting the offside wrong. Call us 'subjective' but Maguire isn't interfering."
A third put: "Inconsistency yet again. It's a subjective call. Surely you can't change that decision on something so flimsy. It's a ridiculous implementation of the rules, being very strict one minute yet in other games they would just let it go."
However, PGMOL chief Howard Webb was pleased with the process.
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"Just being in an offside position in itself isn't an offence. It all depends on what you do when you're in that position," Webb said on Match Officials: Mic'd Up.
"If you touch the ball as an attacker in an offside position or play the ball then that's an offence of interfering with play. That's factual and when that happens, the referee doesn't need to go to the screen.
"But you can also commit an offence without touching the ball as an attacker in an offside position. It all depends on what you do in that position and that needs a judgement by the match officials. It depends whether you interfere with an opponent.
"What we see Harry Maguire do here is attempt to play a ball that's close to him, he challenges an opponent for the ball and he makes an obvious action by moving towards that defender Rodrigo Muniz which impacts his ability to play the ball.
"If you take Maguire out of that situation, Muniz has got an opportunity to clear the ball before it gets to [Alejandro] Garnacho. But it needs a judgement by the officials, so the VAR will ask the referee to go to the screen to make that subjective just like the referee does in all the other subjective areas of the game. A good intervention and correctly the referee was sent to the screen."