The £89m signing appeared to have tweaked a muscle in the pre-match warm-ups and went on to produce a sub-par performance at St James' Park on Sunday.
"No problems," Mourinho told Sky Sports News when asked if Pogba had an injury. "I wanted a better way to come out in the first phase against a team that was defending in a very compact block.
"I was trying that with the simplicity of Michael Carrick because he tries to make everything simple and bring Alexis [Sanchez] close to an area to [Romelu] Lukaku where he could be like a second striker to try to win the game."
When asked about the goal, Mourinho added: "We train, we work, we organise... and the players have their individual jobs when they defend zonal. The players know there are responsibilities but I am pretty sure you already watch that goal on TV a few times, I didn't.
"So you know more than me and you know who lost the challenge in the air, you know clearly that so I think it is bad if you put me in a position where I have to criticise a player. By yourself you make your own analysis."
Man United remain second in the league table but now sit 16 points adrift of leaders Manchester City.