Both players were afforded an extra two days' break at Christmas and subsequently returned to the club later than the rest of the squad.
Messi and Neymar were left on the bench at the start of Barca's La Liga trip to Real Sociedad at the weekend, but were called into action in the second half as the visitors trailed 1-0.
Barca were unable to find an equaliser, however, which led to Luis Enrique being questioned about his decision to rest the pair.
But Ancelotti has backed the decision of his rival.
"I do not know the dressing room of Barcelona, I cannot comment," he said.
"Everyone faces decisions regarding the dressing room. Luis Enrique is best placed to make those decisions, it looked like a fair one.
"I'm not happy [about what is happening at Barca], because I have things to fix.
"I look at my own team, not what happens in Barcelona. Let's just say that teams have problems during the season."
Real next face city rivals Atletico Madrid in the last 16 of the Copa del Rey, with the first leg to come at the Vicente Calderon on Wednesday, and Ancelotti is aware of what to expect.
"We know them very well. We have played against them many times and often this season," he said.
"They are a tough team because they make things difficult for you and they are well organised.
"We have always tried our best to win. They are one of the best teams in Europe."
