Pogba was missing from the United team that faced Huddersfield in the FA Cup last weekend as a result of illness and was omitted from the starting line-up against Sevilla in the Champions League on Wednesday despite being declared fit.
There are already rumours that he might not get back into the team against Chelsea at Old Trafford on Sunday, even though it is one of United's biggest games of the season so far.
Mourinho recently fiercely denied speculation of a falling out between himself and Pogba, describing the gossip as 'lies'. But that has done little to dampen the growing talk in light of the Frenchman's continued absence from the team since.
According to the Daily Mail, Pogba feels he has been treated 'harshly' by his manager and wants to feel 'valued' once more.
The newspaper even claims that his frustration over the situation is such that agent Mino Raiola has already begun 'sounding out' top European clubs over a possible summer transfer.
That is unlikely to be anything more than a warning shot for United at this stage as Pogba has previously been reported to be happy at the club and not looking to leave. But, if true, it is certainly not something that Mourinho and Old Trafford officials can wilfully ignore.
The Sun has further stirred the pot after claiming that a meeting between Mourinho and Pogba ended in a 'furious' row when the United boss apparently reminded his player who was in charge by telling him to look at the 'Manager' sign on the office door as he left.