Los Blancos have been plagued by fitness problems over the course of the season, with Sergio Ramos, Gareth Bale, Karim Benzema and Marcelo among those who have made repeated trips to the doctor's office.
And according to Ancelotti, the plague of problems is a sign of more serious issues within the club.
"The facts show that something is being done extremely badly," the Italian alleged to Sina Sports.
"Since the start of the season there have been 22 muscular injuries at Madrid. Make your own conclusions, but in a club like Madrid that situation does not seem normal."
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Ancelotti, who delivered the coveted Decima Champions League trophy in 2014 before being relieved of his duties the following season, nevertheless stated his faith that rookie coach Zinedine Zidane would solve the injury crisis.
"Of course Madrid need self-criticism, to analyse their mistakes and fix them. I am sure Zidane and the players are doing so," he said of his former assistant in the Spanish capital, while praising Atletico's Diego Simeone.
"They can work it out together. Those who think Atletico and Barcelona are not on the same level are wrong.
"In these three years Simeone has built one of the best teams in Europe.
Cristiano Ronaldo has found himself in the spotlight in the past few weeks, but Ancelotti backed the Portuguese star after his controversial comments following a derby defeat.
"He was talking about his team-mates' physical problems. In fact, there have been too many injuries for Madrid players, it also happened in my last season."