The two forwards have both tasted adversity for contrasting reasons of late as a result of suspension and a lack of playing time
Ronaldo was handed a three-match league suspension after becoming embroiled in an altercation during Los Blancos' 1-1 draw with Athletic in early February.
The 29-year-old courted more controversy when a lighter was thrown at him in Tuesday's 2-0 win over Atletico Madrid in the Copa del Rey, leading Ancelotti to label the situation as "strange".
"I won’t get into that [the 600 euro fine for Atleti]," the coach told reporters. "It’s better not to talk about money. I’d rather talk about the issue of the three-match suspension for Cristiano.
"He isn’t happy, because he wants to play every game. He played well against Atletico Madrid, and now has three days off.
"We submitted our appeal on Tuesday and we’re waiting for the [Spanish Sports Disciplinary] Committee’s answer. It’s strange."
Ancelotti then admitted summer signing Isco has had trouble adapting to his recent tactics, but expects the midfielder's frustration at a lack of playing time to only be a temporary issue.
"Benching Isco is for tactical reasons, because he has difficulties with this system," the Italian continued. "Of course he isn’t happy because he wants to play.
"It’s a temporary problem because he’s an important player. He’s a serious player, he’s professional and there are no problems with him.
"I haven't forgotten that he scored a lot of important goals at the start of the season and won us a lot of points when the team wasn’t in good shape."
The Italian will be keen to leave the off-pitch issues behind him as Madrid travels to face Luis Garcia's men in the hope of securing three points to go back top of La Liga.