The Portugal international had a bust-up with his coach earlier this season after Madrid's 2-0 Copa del Rey win over Valencia and Mourinho has admitted the forward did not take kindly to his comments.
"Ronaldo has had three fantastic seasons with me. We found a tactical set-up where he got the best out of himself and scored a lot of goals. I had one problem with him, though," Mourinho told Punto Pelota.
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"That might be because he thinks he already knows everything and the coach cannot help him grow anymore..."
Mourinho also endured a highly-publicised spat with Pepe during the final stages of his tenure at Santiago Bernabeu, but he insists his compatriot has garnered more support at the club as a result of the dispute.
"I don't know whether Pepe betrayed me. Everybody wanted him out at Madrid, yet I kept him on board," Mourinho continued.
"But he picked up an injury and Raphael Varane did a fine job during his absence. He deserved to play and Pepe didn't adapt well to the new situation.
"All those who called him a murderer before now supported him. I'm happy that he gets that support now. It's great for him and Madrid need players like him."
Mourinho left Madrid at the end of the 2012-13 campaign to return to Chelsea, where he was presented on Monday.