#1 Persisting with the 2 man midfield
It simply was not working, was it? Are there more painful sights in football right now than seeing Paul Pogba play sweeper alongside Nemanja Matic? When Manchester United were constantly playing in the 4-2-3-1 setup, neither of their best players - Alexis Sanchez or Paul Pogba were effective.
More often than not, whenever Pogba pranced forward, he'd end up meddling with Alexis Sanchez's space and this often proved to be counter-productive for Manchester United as they struggled against Newcastle United of all teams.
When they reverted to using Ander Herrera and Nemanja Matic in defensive midfield, thereby affording more freedom to Paul Pogba, Manchester United beat Chelsea, Liverpool, Manchester City and Tottenham Hotspur in the span of 2 months. 2 of those games were played away from home!
Jose persisted with a system that was not getting the best out of his players for far too long and maybe, just maybe, if he had decided to afford the freedom of Old Trafford to Manchester United to Paul Pogba and trust the absolute belligerence of Ander Herrera, Manchester City might not have won the Premier League just yet.