The Italian watched his side coast to victory on Saturday without its talisman but was still unhappy that the Portuguese was unable to play any part
The Portuguese was initially named in Madrid's squad for Saturday's game in the hope his appeal against serving the final match of a three-game suspension would be overturned prior to the clash.
But that bid proved unsuccessful, with Ronaldo forced to watch on from the sidelines. But it didn't matter in the end as goals from Asier Illarramendi, Gareth Bale and Isco secured a comfortable victory.
However, Ancelotti remains unhappy with the treatment of his star man but singled out several of his players for praise following their efforts at the Santiago Bernabeu.
"We played well and won without Ronaldo but I still can't understand why he got suspended. Nobody was happy that he couldn't play. It wasn't normal that he was suspended for three matches," he told reporters.
"Bale's performance was good before the goal but brilliant afterwards. [Asier] Illarramendi had a great game, he is becoming more confident and I am happy for him."
Summer signing Isco again started on the bench but made an impact after replacing Jese Rodriguez in the second half, as he scored his seventh goal in 19 league appearances, with Ancelotti hailing his positional intelligence.
"Isco can play as a central midfielder or as a false nine, which is good for us."
Madrid moved three points clear of Barcelona and Atletico Madrid at the top of the division, but Barca can return to the top when it faces Real Sociedad on Saturday evening, while Atleti is in action against Osasuna on Sunday.