The players were openly critical of match official Alberto Undiano Mallenco following the feisty La Liga fixture that saw Real lose 4-3 to Barcelona after having Ramos dismissed for a challenge on Neymar.
Ronaldo alleged his side "played against 12", while Ramos claimed the result was "pre-meditated".
However, Ancelotti has defended his players' for their comments on Undiano Mallenco, who awarded three penalties on Sunday.
"Cristiano and Ramos did not disrespect anyone," he stressed. "They only expressed an opinion that I understand as well.
"We were unlucky, especially with Ramos' red card. It wasn't fair.
"I don't mind if Undiano Mallenco referees a Real Madrid game again. It's not me who decides.
"Referees make mistakes. That's all."
Ancelotti refused to comment on who he felt should - or should not - officiate the Copa del Rey final between the sides next month, adding: "It's not my responsibility to discuss who should referee the Copa del Rey final. They have a committee for that."
Real are now second in the Spanish top flight by virtue of their head-to-head record with city rivals Atletico, but Ancelotti is confident his side can return to form.
"We trained well," he continued. "The atmosphere is good ahead of tomorrow's important match with Sevilla.
"Tomorrow's match is important because we have to react well after a defeat.
"We've seen many surprises so we know that all the remaining matches are very dangerous.
"The mistakes we made in the Clasico weren't big, they were small details that cost us the game.
"Real Madrid are one of the best teams in the world and we will prove that until the end of the season.
"Sevilla are dangerous because they are going through a good moment. It will be a difficult and complicated match."
