With Mkhitaryan reportedly too expensive for interested clubs Borussia Dortmund and Inter Milan, it seems likely that Mourinho's doubt over his future stems from his involvement in a potential deal for Alexis Sanchez.
Sky are now reporting that, should Sanchez make the move to Old Trafford, that he will receive a basic wage of over £350,000-per-week, adding up to a staggering annual salary of more than £18 million a year.
In addition, Sanchez would be a valuable marketing asset for United in the South American market, with his image rights set to soar if he was to sign for a club that has a vastly superior fan base compared to City around the globe.
Mourinho also said after Monday's game that he was "relaxed" over the move and said he believed United had a "chance" at Sanchez if he leaves Arsenal.
City is unwilling to match the transfer fee and related costs to sign Sanchez that are being offered by United or Chelsea, which is the latest contender for his signature, a person familiar with negotiations told The Associated Press.
United are thought to still be favourites as Arsene Wenger is apparently willing to take United's unsettled Armenian global midfielder Henrikh Mkhitaryan in exchange.
The Red Devils, along with Premier League rivals Liverpool, were said to have been keeping tabs on the 22-year-old's progress at Basel. "A world class player in his peak who can help the club in the Champions League this season".
"He wanted to keep the player clear, saying that he does rate him, but I think he'd happily swap him in any deal for Alexis Sanchez. It's possible. It's also possible he stays".
Mourinho says, "It's the best for him and for us, while the doubt is in the air, to protect him". "The market is open".