Mourinho, who is returning to Chelsea next season after three divisive years at the Santiago Bernabeu, was asked why relations between the two Portuguese compatriots had deteriorated.
"Cristiano had three fantastic seasons with me, all of them," the 50-year-old Mourinho told Spanish television Intereconomia's sports programme Punto Pelota in a recorded interview released Wednesday.
"I think we found a fantastic tactical situation for him to express his potential in goals," he said of the 28-year-old.
"I had one problem with him, very simple, very basic, and it was as a coach to criticize him from a tactical point of view, trying to improve what I believed could be improved," Mourinho added.
"He did not accept it very well because he thinks probably that he knows it all and the coach cannot help him to grow more."
The Portuguese coach had more barbs for 30-year-old defender Pepe, who apparently irked his boss by coming to the defence of Real Madrid's benched keeper Iker Casillas.
Mourinho claimed he was responsible for keeping Pepe at Madrid and fighting for him to get a good contract.
But he said Pepe had reacted badly to competition from 20-year-old French player Raphael Varane, who snatched his place in the Real starting line-up.
"A kid who was 10, 12, or 13 years younger than him started to play, but a kid who in my opinion deserved to play. And I think he did not assimilate or accept that situation well," Mourinho said.
Suddenly, all the critics of Pepe's aggressive playing style had become his defenders, the coach said. "From one moment to the next, they all went to his side and defended him to the hilt."
Mourinho, who returned to the London club he previously coached from 2004 to 2007, had a positive review of his own role in Madrid.
"If you ask me if I would go to Real again knowing what has happened in the last three years then I say that I would do so. Because if I had not come I would not be able to say that I had won the three most important championships of the world," he said, referring to the titles he picked up with Chelsea, Inter Milan, and then with Real Madrid in the 2011/12 season.