The Spanish international joined Los Blancos from Malaga in the summer and impressed during his first few months in the Spanish capital.
However, the midfielder has struggled for regular football in recent months after Ancelotti settled on a 4-3-3 formation, with Angel di Maria the preferred attacking option from central midfield.
"Ancelotti has not been fair with Isco," Antic told Goal.com.
"Ancelotti keeps on pointing at the defensive aspect of Isco's game. I think he's a tremendous player who adds something vital to the team: creating chances against a defensive opponent.
"Ancelotti is always looking at the player's weaknesses and this does not help to get the best out of Isco."
Isco has scored 11 times for Madrid this season.