I could be wrong but I suspect that something happened after the first match against City. You don't play someone in such an important game if you don't trust him, and he was getting minutes before as a substitute. And I don't think it's something related with the level of that performance, because Lingard was awful and subbed at half-time too but he's been playing after that.
Mourinho said something after the game about some players being mentally weak, and maybe Mkhi didn't take it in a good way. It was his first start and he was carrying an injury, so he probably felt that he was being unfairly thrown under the bus. There you have the ingredients for a confrontation. Even in the press conference against Watford, Mourinho kept insisting on the fact that Mkhitaryan didn't press well in the first goal against City. Maybe players like Lingard, Shaw are more tolerant in that regard, and Mkhitaryan reacts differently to this kind of things.
I'm just guessing of course, but I can't buy the reasons about 'match fit', 'adapting to the league', because you improve with game time and he's not getting it. Yesterday it was the perfect chance to give him 20-30 minutes and he wasn't even on the bench. I wouldn't be surprised if he starts playing again at some point, but it looks like personal differences to me, more than a football thing.