Continuity mistake: When the kids first react to Delores scraping her nails on the blackboard, a girl near the front of the class, (later revealed as 'Maria') wearing sunglasses, is in the process of sitting in a chair. When Delores then asks them to put the desks back, she is now sitting on top of a different desk further to the right, is now holding a magazine and no longer wearing sunglasses. The short time elapsed makes it impossible for her to have moved.
Audio problem: At the contest in Hollywood, when the priest pushes Mr. Crisp into the closet he says, "Forgive me," but his lips don't move.
Continuity mistake: When the sisters are counting the money after their charity concert, Sister Mary Clarence puts a bunch of singles on top of her legal pad right before she talks to Kathy Najimy. When the shot changes the singles are not on top of the pad anymore, but a little further up on the table.
Continuity mistake: When Whoopi Goldberg is pushing herself along the walkway after she is stuck to the chair, you can see her move out of view on the camera angle. They then have the angle from in front of her, still pushing herself along the walkway. They then go back to the previous angle and she is back where she started from without rolling backwards.
Plot hole: Even though Rita left the choir early into rehearsal for the contest, and her mother took her music away to prevent her practising before she had learned it, she still manages to know the song by heart and the dance routine perfectly when she rejoins her friends last minute. She couldn't have perfected her performance in the time she had.