Preparations for Tuesday's Carabao Cup match against Derby were disrupted by claims that the club-record signing's tense relationship with the manager has reached a new low.
Pogba was not pictured with the United squad ahead of the third-round tie and was reported by the Times and ESPN to have been told earlier in the day in front of the squad that he would not skipper the side again as he does not embody what the club is about.
United were not able to comment on the matter, but the incident was expected to be broached with Mourinho before or after the match against Derby.
Mourinho is 7/1 with Sky Bet to be the next Premier League manager to leave his job, with Zinedine Zidane favourite to replace him.
Sources close to the club were not surprised by the latest development, which will only increase speculation as to whether Pogba will stay at Old Trafford.
The France international captained the side in the Premier League openers against Leicester and Brighton in the absence of Antonio Valencia, just as he did in last week's Champions League win at Young Boys.
Pogba scored two and set up the other in the 3-0 victory in Switzerland, only to under-perform on Saturday's return to league action against Wolves.
The 25-year-old was dispossessed in the move that led to Joao Moutinho's equaliser, with the midfielder saying afterwards that United should "attack, attack, attack".
Those comments are understood have got under Mourinho's skin, while Pogba took umbrage at the way they were reported.
"Some people make polemic even from 'good morning' to create drama," he posted on Twitter. "Big Pogoodmorning everyone hope u get it twisted."
Fast Results
Scores
Racecards 
