Dimitri Payet should have had a clear penalty and was inexplicably adjudged to have fouled Varela when through on goal before Anthony Martial scored a late equaliser despite a clear foul on Hammers 'keeper Darren Randolph.
Slaven Bilic's side were forced to settle for a 1-1 draw that day and a replay.
But just when fans thought it couldn't get any worse, it did.
'Cheated, robbed, mugged'
At Stamford Bridge, where the Hammers haven't won since 2003, they were deservedly and comfortably leading fierce rivals Chelsea 2-1 and looked set to leapfrog Manchester City into the Champions League places.
That was until another howler from the match officials saw the Blues awarded a penalty that never was in the dying seconds of the game.
It wasn't the only controversy either.
In first half stoppage time the referee pushed the Hammers wall back 12 yards, with the protestation of West Ham's players going ignored. Fabregas stepped up and converted the free-kick, made all the easier for him with West Ham's wall completely powerless to stop it.
Frustrating and unjust for the Hammers, but some of the blame also lay closer to home.
Naivety just as costly
Bilic's brilliant side showed a touch of naivety in both matches.
At Manchester United the players barely appealed the foul on Randolph and decisions on Payet. In many ways that is admirable but their politeness could end up literally costing them silverware.
Against Chelsea when the ref refused to relent over the distance he had made the wall retreat, why didn't Adrian take up a more central position given his wall was ruled more or less useless?
And the biggest question of all, why oh why were the Hammers attacking in great numbers in the last minute while winning 2-1 leaving huge gaps at the back for Chelsea to exploit?
All questions which will be eating away at Bilic and the Hammers fans in the coming days when the anger over the performance of the officials subsides.
Hammers fans will forgive a little naivety from their side , though, given it is the best West Ham have looked since probably as far back as 1985/86.