Ander Herrera was replaced at half-time on Sunday and Ashley Young was taken off in the 75th minute, while Paul Pogba was withdrawn in the 58th minute.
The France midfielder was a shadow of the imposing, match-winning presence seen in the second half against City.
“It was not just him,” Mourinho said of Pogba’s performance.
“We weren’t good enough. It is not ideal, but we need to keep that second position and fight to be in another FA Cup final, and try to win it.”
— Manchester United (@ManUtd) April 16, 2018
“And he had a yellow card, so he was in a more difficult position than others.
“And playing with only two midfield players, you cannot play with one player in risk of not being able to make a foul.
“You can do it if your team is not losing the ball, but our team was losing the ball so easy with the complication, everything was complicated, so we were losing lots of balls.
“So, by losing lots of balls, with turnings and flicks and tricks, the midfield players and central defenders are at risk of one touch, one late challenge and they are out.