Fernandes was sent off in the 42nd minute for a high challenge on James Maddison at Old Trafford last month but later avoided a three-match suspension after United successfully appealed the red card.
"We released the audio, you can hear the assistant referee — who's got a good view of it — just saying, 'that looks awful, 100% red (card) for me'," PGMOL head Webb said on the Stick to Football podcast.
"From his angle it looked it, because it looks like the studs have gone in. But then there's another angle shown on the replay on Sky Sports. Straight away I've gone, 'that'll be an overturn', but it wasn't.
"I was frustrated that we didn't step in to rectify it because it was clearly wrong in my opinion and he didn't drive the studs in. If he had then it would have been a red card."
VAR was introduced in 2019 to assist on-field officials with key match decisions but the technology has been at the centre of controversy with complaints ranging from its extensive analysis to delays that can take several minutes.
Teams voted in favour of keeping VAR in June despite huge amounts of criticism about the technology-aided officiating system last season.
Webb said VAR had made far fewer errors this season.
"We have this independent panel which has got ex-players on it, and they judge each decision each week, and according to the panel — which is independent from us (PGMOL) — there has only been two VAR errors this season compared to 10 at the same time last year," he added.
