However, Ronaldo is still confident that his side will win the La Liga title this season.
"We played against 12. It's always the same. They don't allow us. Maybe they wanted Barca back in the League," he told reporters.
"I don't want to leave this inside of me and I'm not looking for excuses, but the ref is not at the required level for a game like this. If Barca lost today they would have been out. After five years here, I understand how things work.
"[The media] has been here for many years more than me. I have never seen Real Madrid favoured by the referees. I'm sure that no matter all this, we will win the League."
Sunday's defeat ended Madrid's 31-match unbeaten run in all competitions.