The Armenian international started the season in fine form by bagging a number of assists as the Red Devils began the season in fine style.
However, the midfielder has been left out of the match day squads to face Arsenal, Manchester City, Watford and Bouremouth.
"I can only have six [outfield] players on the bench and I try to have some balance on the bench," Mourinho told reporters.
"I had two defenders and [Daley] Blind who can play in different areas. I had Ashley Young to cover me all the wings and the wing-back position.
"I had [Ander] Herrera as a midfield player, Zlatan [Ibrahimovic] as a striker and Marcus [Rashford] as a second striker and winger.
"I played [Anthony] Martial, [Juan] Mata and [Jesse] Lingard in the team. To have Mkhi means that I don't have one of them and, in this moment, I believe the other ones they deserve [the chance to play]."