Mourinho believes manager Ole Gunnar Solskjaer made wrong choices during the match, leading to the loss that eventually tossed them out of the competition.
"I think the United approach was different," Mourinho told Russia Today.
"In the first leg, they tried to occupy that central zone. Messi’s position is easy to understand but it is not easy to create a ‘cage’ to control him. He comes from the right, then stays in the middle, then Rakitic goes right and allows him to stay in the middle. It’s very difficult,"
"But I think in this match because United were losing 1-0 they tried to start with a different perspective,"
"Now it was Pogba wide left, McTominay much more on the right and Jesse Lingard starting as a 10 behind the strikers. In front of the defensive line was only Fred. That’s the area that Messi comes to get the ball and when Messi has the ball..one, one, one…you are dead,"
The defeat was the fifth in the last seven matches for United, marking a difficult period for Ole Gunnar, who started his reign at the club brightly.
Ole Gunnar will lead his boys on Saturday when they take on Everton at the Goodison Park in a must-win English Premier League match.