The coach was not surprised the hosts' spirit was dented after the Portuguese's early goal and defended Fabio Coentrao following his sending off in the cup tie.
The Portugal captain scored the opener from a free kick after the hosts' goalkeeper Andres Fernandez fumbled a punch through his own legs.
Angel Di Maria's second-half strike finished off the Copa del Rey last-16 clash, as Madrid triumphed 4-0 on aggregate, but they did end the game with nine men after Fabio Coentrao was sent off and Alvaro Morata forced from the field with a facial injury.
Ancelotti was pleased with his side's control of the game and spoke out in defence of Coentrao for what he believes was a harsh dismissal.
"They started as we expected, with intensity and pressing high up, but after Cristiano's goal it was very difficult for them," Ancelotti told reporters after fulltime. "We were always in control of the match and the team managed to score early on. Defensively we were solid and, from that foundation, we were able to score twice.
"I do not think Morata's assessment is too severe. His eye is inflamed by the blow to the shoulder but nothing more. Coentrao was unlucky with the expulsion, he played very good. He was focused and before the expulsion made no mistakes."
Madrid, which will face Espanyol in the Copa del Rey quarterfinal stage, travels to Betis on Saturday for its next Liga clash.