Manchester United’s £89million star has been dropped and had heated touchline discussions.
But Pogba, talking as Mourinho’s No 2 Rui Faria confirmed he is quitting United, said: “Sometimes I see things he doesn’t and sometimes he sees things I can’t.
"But it doesn’t mean anything is bad. It’s good.
"You see some images of me talking with the coach. We can disagree but he is still the manager and I am the player.
“He is the coach, he decides and I accept and I respond on the pitch.”
Pogba has started United’s last eight games as they sealed second place in the Premier League and reached next weekend’s FA Cup final.
But Mourinho will be in no mood for celebration — even if they beat Watford at Old Trafford today and go on to lift the Cup against Chelsea at Wembley.
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United are 19 points adrift of champions Manchester City and Mourinho said: “Is it enough to celebrate? No, not for me.
“The difference in points tells a lot. I always think that in the championship the truth is always there.
“In knockout competitions, in one bad day, sometimes in a lucky or unlucky moment, the truth is not always there.
“Over 38 matches, the reality is the numbers. The difference between second and fifth is only a few points but between first and second is 19.
“Can we close that gap in one season? We are going to try.”
Faria is ending his 17-year association after being offered a management start in Saudi Arabia, although Turkish giants Fenerbahce are another possible destination.
Mourinho said: “Seventeen years — in Leiria, Porto, London, Milan, Madrid, London again and Manchester.
“Training, playing, travelling, studying, laughing and also a few tears of happiness. Seventeen years and the kid is now a man.
“The intelligent student is now a football expert, ready for a successful career as a manager.
“I will miss my friend and that is the hardest thing for me. But his happiness is more important — and, of course, I respect his decision.”
Faria said: “With a very heavy heart, I have decided the time is right for me to move on.
“I have had 17 years of incredible and unforgettable experiences.
“My heartfelt thanks go to Jose Mourinho, for the belief he had in me, all those years ago, when it all was just a student dream.”
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