Arsenal were leading 1-0 when Callum Wilson struck a last-gasp leveller in extra time that sent the London Stadium into frenzy.
However, referee Chris Kavanagh was sent to the monitor to review the incident and after 17 replays, totalling four minutes and 17 seconds worth of stoppage, he ruled out the goal.
This came as Arsenal goalkeeper David Raya was supposedly fouled in the build up, a decision that is one of the most controversial moments of the season that has a huge impact at both sides of the table.
Speaking on the decision, Nuno revealed that there has to be more clarity with VAR calls as what is and what isn’t a foul is not clear enough.
"They have to solve it. They have to come to the clubs and explain and show why sometimes it is, sometimes it's not. Sometimes it's a goal, sometimes not a goal.
"Everybody feels confused. Today we are upset, we are sad. It's the lack of consistency with the decisions.
"These previous recent seasons have been having a lot of blocking, grappling, holding. Almost like a wrestling situation that all of us don't even understand what is a foul, what is not a foul. I think even the referees confuse themselves.
"Not only today but in all the pitches. Everybody, us included, are trying. But what is the barrier, what is the frontier of what is a foul and what is not a foul? It is tough.”
The Gunners now require just two further victories to be crowned Premier League champions whilst West Ham are still in a huge relegation fight with just 3 games of the season remaining.