Mourinho will be without Ricardo Carvalho for the first leg against Barca after the Portugal defender triggered a suspension when he was booked for a foul on Tom Huddlestone in Wednesday's 1-0 win over Tottenham in the quarter-final second leg.
The Real boss, whose side went through 5-0 on aggregate, admitted he could have avoided that situation by telling Carvalho to deliberately get booked when his side were 4-0 up against Spurs in the first leg.
That would have ruled Carvalho out of the second leg at White Hart Lane instead of leaving him vulnerable to a semi-final ban.
But Mourinho opted against that tactic as he had already been hit with a suspended one-match ban by UEFA, European football's governing body, after allegedly telling Xabi Alonso and Sergio Ramos to get booked in a group match against Ajax earlier this season so they would get rid of a suspension before the knockout stage.
Undoubtedly with Barca in mind, Mourinho hinted that another club had been allowed to get away with a similar move.
That was apparently a reference to a booking for Barca's Andres Iniesta against Shakhtar Donetsk that earned him a second leg suspension but meant he would be able to play the semi-final.
There was also an incident which saw Barca duo Victor Valdes and Sergio Busquets booked for time-wasting in a recent league match - ruling them out of the next game, but leaving them free to face Real on Saturday.
"Maybe you have to find a reason why Mourinho can't clean yellow cards and other clubs can. I can do nothing about it," Mourinho said.
"To be honest, as I always am. when we scored the fourth goal in the first leg my assistant told me 'get yellow cards for Cristiano Ronaldo and Carvalho'.
"I said no way because I would be suspended for the semi-finals. Then the next day when we are at home, another coach did it.
"It was always going to be problematic going into the game with three defenders on yellows and risking missing the next match.
"Some teams can clean up their situation with yellow cards and other cannot."
The semi-final between these age-old rivals will be one of four matches in the space of a month that will determine whether Mourinho's first season at the Bernabeu will judged a success.
Real have fallen well behind Barca in La Liga and face a must-win clash against Pep Guardiola's team on Saturday. They meet again in the Spanish Cup final on April 20 before heading into the two Euro meetings.
"In a semi-final anything can happen. They have a great situation with the suspensions, which we don't. But we will fight," Mourinho said.
"We have two matches against them before the semi-finals, so we have to look at those games first.
"We have to take each game as a separate entity. I'm not of the opinion that what happens in the first game can influence the second, third or fourth."
Taking a team to their first Champions League semi-final for eight years would be a significant achievement at some clubs, but Mourinho knows only securing Madrid's tenth triumph in the competition would be enough to satisfy his demanding employers.
"I know you are judged by your results," he said. "If you don't win titles it is easy to forget all the good work that has gone before.
"But I don't think it would be considered a good season to get to the final of the Spanish Cup and the semi-finals of the Champions League.
Inevitably on one of his rare returns to England, former Chelsea boss Mourinho was asked if his future lies in the Premier League.
"It is my natural habitat," he said. "It is where I want to come... after Real Madrid. I stay in Real Madrid next season, unless the press sacks me."