Mourinho says the club were simply trying to keep their unhappiness to themselves after previously being criticised for voicing their complaints.
"Last season, after the Champions League semi-finals, we said what we thought with open hearts and you lot (the media) killed us," he said.
"You criticised us again after we criticised the referee when we were eliminated from the Copa del Rey this year.
"We wanted to avoid controversy and suspensions after facing Villarreal and that is why we didn't make any comments.
"We thought we were doing what was best, but we've been criticised again. We don't have any problems, you cause them and have to decide which of the two attitudes is better.
"You cannot accuse us of looking for controversy this time because we kept quiet. I don't know if you're fixated on me or on Real Madrid, but we're always criticised. We nevertheless believe we did the right thing and neither I nor my players said anything against the referee."