All of this comes on the back of reported rifts within the United squad, with Mourinho's relationship with the likes of Paul Pogba, Anthony Martial and Luke Shaw all being questioned in recent months.
United manager Jose Mourinho said he felt his team were in difficulty once the shootout got down to his defenders.
"That's Old Trafford", Pogba was quoted as saying in his post-match interview.
Paul Pogba cut a frustrated figure at Manchester United training on Wednesday.
He told Sky Sports: "The only truth is that I made the decision of Pogba not to be the second captain anymore".
Mourinho made Pogba the most expensive player in history when he signed him from Juventus for £89.3million in 2016, but his form over two completed seasons since returning to Old Trafford has been patchy.
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Mourinho insisted that there was "no fallout at all, no problem at all, just a decision that I don't have to explain". They played so well against Brentford and I knew how much they all wanted to play.
But according to ESPNFC, United's senior players are "angry and frustrated" with Pogba being stripped of the captaincy, and the French player reportedly also being vocal about wanting a more attacking style of play at the club. "It's not me. I'm not the manager, I can not, like, say that, but obviously we should show more options of playing".
After taking the lead through Juan Mata, a terrific Harry Wilson free-kick and a Jack Marriott goal turned the game on its head.
Manchester United will make the daunting trip to West Ham United at the London Stadium in the Premier League at the weekend. Pogba was smiling and giving high-fives, but that all changed when Mourinho said something to Pogba.
The latest clash between the two figures comes after Mourinho stated that he had removed Pogba as the "second captain" at the club behind Antonio Valencia.
As a result, sources have said a number of players are prepared to consider a future away from United next summer if the situation does not improve.