An unspecified illness saw Pogba withdraw on the morning of Saturday's match in Huddersfield, which United won 2-0 thanks to two goals from Romelu Lukaku as they advanced into the quarter-finals.
United manager Mourinho, whose relationship with club-record signing Pogba has been under close scrutiny in recent weeks, insisted he did not even know what the illness was or how long the France midfielder may be unable to play, having planned to play him in a 4-3-3 system that the player considers his favourite.
"I don't know," said Mourinho when asked about the nature of Pogba's illness after Saturday's match. "When I was told by the doctor this morning that he was not coming, I don't want to know anything else about it — I have to think who is going to replace him, what I am going to do because we worked hard during the week. Now is the time to think about Paul, to know what happened, why he didn't feel good enough to play, can he play or be available to help us on Wednesday?"
Pogba has reportedly been unhappy in recent weeks at the style Mourinho has adopted, generally playing him alongside Nemanja Matic in a two-man midfield.
But ahead of Saturday's match, Mourinho appeared prepared to meet the wishes of Pogba by playing him on the left side of a three-man midfield set-up.
United still won comfortably, thanks to Lukaku's double, although victory could have been even more emphatic but for video assistant referee (VAR) Neil Swarbrick ruling out a Juan Mata 'goal' late in the first half in an incredibly close offside call.
"It was my first experience on the bench but we have VAR in Portugal," said Mourinho. "It is amazing when the truth comes but also [here are] problems like what happened today which go against the words of the protocol. The words of the protocol are something like a 'clear and obvious situation' and for sure it is not a clear and obvious situation, but we know it is experimental and we have to accept.”
Although Wagner's side benefitted from the VAR in this instance, the Huddersfield manager said he was against the experimental system.
"I said immediately to Jose, during the incident, whatever is decided, whether it goes in our favour or not, I don't like it," explained Wagner. "The emotion is killed, the emotion in the stadium, the stands, for us in the dug-outs. It is killed. That's why I don't like it.”
United have been drawn to face Brighton in the last eight — a tie that revives memories of the 1983 FA Cup final when they eventually defeated the Seagulls after a Wembley replay.
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