Mourinho branded his side the "masters of complication" as they lost at home to the league's bottom team.
The Portuguese has not been shy in criticising his players during the 2017-18 campaign, and Francis has said that he agreed with Mourinho's comments following the Baggies match.
"You cannot fault what he has done and what he has achieved. The medals he has won, the trophies he has won in all different countries," Francis told Sky Sports News. "He is a phenomenal manager in terms of winning things. He does things differently to how I would do things in terms of the players.
"Generally for me it was always an in-house situation as in 'we were good' or 'we were bad' but Jose seems to change that around sometimes as in 'they were poor but I'm still good'. He does what he does and he has been very successful in doing that so can you fault him?
"I watched the West Brom game and I agree with him 100%. United were overindulgent on the ball, they took too long and were slow in their build-up. There were too many flicks and messing around and he was absolutely right. In many cases they got what they deserved on the day. West Brom did very well."
United will look to return to winning ways in the Premier League when they travel to Bournemouth on Wednesday night, before taking on Tottenham Hotspur in the semi-finals of the FA Cup this weekend.