That meant the East Londoners finished seventh in the Premier League allowing Southampton and United to leapfrog them into the Europa League spots.
But with the Old Trafford side having already qualified by virtue of league position, their place for winning the cup passed down to the next team in the table without it.
However, according to unconfirmed reports online, West Ham could now face an issue with where to play the third qualifying round home leg come the summer.
Olympic Stadium issue
That's because their new 60,000 seater Olympic Stadium home is in the hands of UK Athletics the week the two-legged tie is meant to be played (July 28th and August 4th), as reported by the likes of the Daily Mail.
The stadium takes seven days to convert from athletics to football mode and is only due to be handed over by UK Athletics to West Ham on August 1 after the London Anniversary Games and other events.
It means the club may either have to request permission from UEFA to switch the home tie to the second leg after the handover, or play the match at another ground.
One last Upton Park hurrah?
That could leave open the possibility for a romantic last hurrah at the club's beloved Boleyn Ground, which has been sold to developers for housing.
Although an auction is currently under way to sell off everything of note from Upton Park including the seats, it could prove an ideal solution despite the club and fans believing the thrilling 3-2 victory over Manchester United was the last ever game there.
It is not yet known whether it would be a genuine possibility but surely it is the ideal solution to what is a real problem, particularly given the draw for the Europa League third qualifying round is set to be made on July 15, giving West Ham less than a fortnight to confirm arrangements.
Fans voice concerns
Fans have taken to Twitter to voice their concerns over the issue to Hammers co-owner David Gold.
One supporter suggested it would not be a problem if the club owned its own ground to which Gold responded: "Paul there are very few clubs that own their own grounds most are owned by there banks."
Paul there are very few clubs that own their own grounds most are owned by there banks. dg https://t.co/aK0Q4DWhcx— David Gold (@davidgold) May 21, 2016
The official opening of the stadium remains a prestige friendly against Juventus which takes place on August 7.