#1 Injury prone & inconsistent United defense

Mourinho never got a chance to play a consistent back line this year. He has Chris Smalling, Phil Jones, Eric Bailly, Marcos Rojo, Victor Lindelof as center-backs, but their frequent injuries have made Mourinho to chop and change the team on multiple occasions.
Eric Bailly had a brilliant year but only played a limited role because of his frequent injuries. The same goes for Phil Jones and Marcos Rojo as well. Chris Smalling was inconsistent and Lindelof took a lot of time to settle at Old Trafford.
Even though Mourinho had 5 center-backs in the squad, he rarely had the luxury to pick his best two. If not for David de Gea's brilliance, Manchester United's defensive record would have looked really bad.
The same goes for full-backs. Except for Antonio Valencia, United played Matteo Darmian, Daley Blind, Luke Shaw, and Ashley Young as full-backs during the last few months and none them showed quality except for Ashley Young.