Juan Mata's goal was ruled out following a lengthy stoppage.
The VAR system faced criticism again as Manchester United had a goal contentiously ruled out for offside by the video assistant in their 2-0 FA Cup fifth-round victory over Huddersfield Town on Saturday.
United midfielder Juan Mata put the ball in the net on the stroke of halftime with his side already leading 1-0 but his effort was eventually ruled out following a lengthy stoppage.
The goal had initially been given after the linesman had kept his flag down, but after long-winded deliberations with the video assistant, referee Kevin Friend scrapped his original decision.
Replays suggested that if Mata was offside, it was only by the tiniest fraction and not a clear mistake by the officials.
Despite having the goal chalked off, Spaniard Mata said he was in favour of the VAR system, but Huddersfield manager David Wagner, whose team benefited from the decision, said it was "killing the emotion of the game".
"I think the line was very tight," Mata told the BBC after two goals from Romelu Lukaku sent United into the quarter-finals.
"I did what I had to do which was to score and celebrated. Then after I saw the referee speaking to someone and you look silly when the goal is denied.
"I'm up for VAR and I think it is good for football especially to make important decisions and make it a little bit fairer but it seems like today it was not a very clear the decision against us and me."
Wagner was less enthusiastic about VAR even though it kept Huddersfield in the match before Lukaku, who gave United a third-minute lead, sealed their victory with another clinical finish following a defence-splitting pass by Alexis Sanchez.
"Yes, the decision went in our favour but this VAR for me kills the emotion of the game," he said.
"This is why I don't like it but I am not the person who makes the decision."
With one eye on Wednesday's Champions League last 16 first leg away to Sevilla, United manager Jose Mourinho rested several starters and was happy after his makeshift side, also missing the ill Paul Pogba, cruised into the last eight.
"It was hard but we started really well," said the Portuguese coach, who denied reports earlier in the week that he was at loggerheads with the out-of-form Pogba.
"With that second goal in the second half I think we killed the game and from that moment we were in control.
"Good counter-attacks, twice attacking the space well. Twice cold in front of the keeper, good decisions, good shots, good goals, important goals from us."
United will host Brighton and Hove Albion in the quarter-final.
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