He picked Valencia in midfield rather than at his usual right-back role while Mata was replaced with Marcos Rojo after 69 minutes on the pitch.
Mourinho insisted the fact that he didn’t have any midfield players on the bench also effected his judgement as he tried to come up with a plan to counter the busy schedule of fixtures.
Speaking about the pair, Mourinho claimed he had to keep them safe to counter the effects of three games in seven days after clashes with Chelsea and FC Rostov.
“We change a lot of players,” he said.
“We had to do that. We tried to protect others with the way we played. For example Valencia played in position where I tried to protect him a little bit. Instead of 100m up and down, 50m up and down.
“I tried to protect the central defenders in the last part of the game bringing another one. I had to protect Mata after 60 minutes because he played 90 against Rostov.
“I had no midfield players on the bench so I had to go with Carrick and Fellaini for 90 minutes for sure because we didn’t have another one.”
Man United will now take part in the international break with most players set to play a role, but once they get back, the squad will play 16 times in 54 days after the international break if they make the Europa League final.
Mourinho still has a massive task ahead and will need to continue to rotate his players to ensure they remain fighting fit.