The Armenian playmaker has struggled for regular game time under Mourinho and the indignation of being taken off at half-time during Friday night's FA Cup third round clash at Old Trafford has fueled talk of a January exit, especially as he wasn't playing that badly at the time.
But after the game the Red Devils managers moved to explain his decision to remove the midfielder who has not complete 90 minutes in any of his 11 starts this season, and even brought with it a rare apology from the usually unrepentant manager.
"[It was] unfair [to take Mkhitaryan off] and I told him that at half-time," Mourinho said.
"I didn’t like what I did. He didn’t deserve it, he was playing well, he wasn’t playing bad.
"He had a couple of missed passes but he was playing well and giving a good dynamic to the team."
Mourinho replaced Mkhitaryan with Romelu Lukaku who went to on to score United's second goal in a 2-0 win after Jesse Lingard had opened the scoring to continue his purple patch over the new year.
The Portuguese coach added: "My feeling was just that [Marcus] Rashford is not going to score a goal and because of that I’m not going to lose time and I’m going to play Romelu, so then I had to sacrifice a player.
"Mkhi was the one that I sacrificed but it’s something that I don’t normally do but I did at half-time and apologised to him in front of other people because he didn’t deserve it."
It's a different sort of tone from the one Mourinho had on the 28-year-old outcast back in November when he publicly questioned the midfielder's form, saying: "I was not happy with his last performances. I'm not speaking about one or two, I'm speaking about three, four or five."
Mkhitaryan's career at Old Trafford has been typified by a lack of proper playing time, despite some good form in patches, meaning he has been linked with a move away this month. According to Sky Italia he has already turned down the chance to leave for Inter Milan while Borussia Dortmund - the team he left to join Manchester United in 2016 - are also said to be interested.
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