I've said it before and I'll say it again this situation does not surprise me one bit, the writing was actually on the wall before the seasons even started given he barely played in pre-season despite being one of the few players who didn't play for his country in the summer.
Jose has a history of this (especially at Chelsea), Salah, Cuadrado, Luis and I'm sure there are others, players Jose signs and never gives a chance to. I'm not sure if he does it to make a statement that no player is untouchable (even his big money signings) or whether he just doesn't scout players very well and ends up buying players who when he then works with decides they're not for him, either way I'd be very surprised if Mkhitaryan is anything more than a bit part fringe player for us this season before being loaned out or sold in an upcoming transfer window