When Sister Mary Clarence is running through the kitchen to escape from Joey and Willy, they shoot at her as she starts up the stairs. Approximately one second elapses between the shot and the ricochet off the stair railing. In reality, at the distance the shot was fired, the ricochet would have been almost instantaneous.
In the first scene, young Delores' teacher asks her to write the names of all the apostles on the blackboard, alphabetically. Delores writes "John, Paul, Peter, Elvis." Until she writes "Elvis" the teacher is nodding in approval. Two things are wrong with this. First, Paul (though considered an apostle in a different context) is not one of the original twelve apostles. Second, when the apostles are written alphabetically, "Andrew" is the first. Any Catholic school teacher would have corrected her long before she added "Elvis" to the list.
When Sister Mary Roberts gives Sister Mary Clarence the clock to help her wake up in the morning, you see Sister Mary Clarence's hand reach out for clock. In the next shot, Mary Clarence's hand reaches out for the clock again.
During the credits at the end of the movie, the spelling of Deloris's name rotates between Delores and Deloris on the magazine covers. The first two magazines (People and Newsweek) show "Delores," while the second two, Time and the National Enquirer show "Deloris".
When Lt. Souther delivers Deloris to the convent, he tells her that Vince has a $100,000 contract on her. A few scenes later, however, when Vince and his crew are leaving the police station with the lawyer, he only then realizes Lt. Souther has Deloris and puts the contract on her.
When Sister Mary Clarence/Dolores is meeting with the Mother Superior in her office right after the first choir performance in which she is choir mistress a crewmember's hand can be seen trying to get the pigeons to stay on the window sill.
When Sister Mary Clarence/Dolores is escaping from Joey and Willy, towards the end of the film, she is shot at. We hear the shot but, although the pistol is on screen at the same time, we don't see it being fired.
The goof item below may give away important plot points.
The story revolves around the idea that Deloris saw Vince LaRocca kill someone and can therefore testify against him in court, so Vince must do away with her or go to prison. Yet, in the casino, he is prepared to kill her in full view of all the nuns. This means that he would then have to kill all of the sisters since they could now testify against him for killing Deloris.