Plot hole: Delores is walking into the murder scene at the beginning of the movie just as Ernie is shot. Later, while she is being questioned, she tells the two detectives what the thugs said and did, yet, she was not eavesdropping or looking through the door.
Visible crew/equipment: When Eddie arrives at the casino near the end of the film, he opens the car door and in the reflection you can see the filming crew.
Other mistake: When Whoopi first takes over the choir, she asks the sisters to stand according to their singing voices. She asks where the sopranos are, and several women on opposite corners of the grouping raise their hands. She asks them to all move over to the left group, but only one of the two women on the right side actually does so.
Factual error: At the very end of the movie, the Pope gives the nuns a standing ovation. The other people seated in the box with him should have immediately risen at this time. Instead, the man seated to his left looks up at him, seeing that the pontiff has stood, but makes no movement to join him on his feet.
Plot hole: In the scene where the limo driver gets shot, Deloris walks in just as the bullet is fired. She doesn't see what happened before, just the guy getting shot. However, when she is telling the police what happens, she tells them that Vince looks at Ernie and says 'Good night.' He did, but she wasn't there at that point.
Character mistake: At the very beginning of the movie, young Delores' teacher tells her to go to the board and right down the names of the apostles alphabetically. Delores writes down, John, Paul and Peter with the nun nodding in approval until Delores writes down Elvis. Paul wasn't one of the original apostles and since the nun told Delores to write it down alphabetically, the first name on the board should have been Andrew but, the nun doesn't stop and correct Delores after she writes John's name down first.
Continuity mistake: When Willie and Joey are pointing their guns at Delores in Vince's office, they count to three, waiting for the other to shoot first. In the close-up shot, Willie's gun is closer to Delores' head than it was in the previous wide shot.
Factual error: At the end of the movie when they put on the concert for the Pope, Dolores is no longer wearing a full habit as her hair and ears (with big hoop earrings are visible). She isn't wearing a full habit because she would not have been allowed to, especially in the Pope's presence, since it was made public that she's not really a nun. However, during the end credits there is a picture of her with the Pope, and she is wearing a full habit.
Continuity mistake: The number of nuns in the choir changes between when Mary Clarence joins, the later casino scenes, and the end concert for the Pope. At the start, there are over 20, and by the ending, there are about 12-15.
Continuity mistake: When Deloris is on TV, we see her lift a stuffed rabbit to try and hide her face, she then gives it to Mary Robert and lifts the kid to her face but when Eddie says "I'm gonna kill her. I'm gonna kill her myself", if you look on the TV, you can see her doing the exact same thing again.