Revealing mistake: After Mary Robert jumps out of the car, you can see the stunt double falling for her.
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.
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.
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.
Continuity mistake: When the choir are singing the first song that Deloris helps them with, Sister Mary Robert gains confidence and sings louder. Toward the end of the song, she puts her hands together in a praying gesture while she is singing loudly, but in the next shot her arms are by her side.
Character mistake: During the end credits, three of the magazine covers spell Whoopi's character's name as "Delores." Two of the covers spell it "Deloris," as do the credits.
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.
Other mistake: During the 'Rescue Me' montage, when Maggie Smith catches Whoopi Goldberg singing whilst washing the car, Whoopi reacts to her and then there's a brief moment where she looks straight at the camera.
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: The very first second we see old Deloris, during the opening credits, she holds the mic with her right hand, then lowers her left hand. A shot later, her left hand is now on the mic, and the right hand is grabbing the microphone stand.
Deliberate mistake: When the nuns sing for the first time in the church in perfect tone then break into the dance version of the song, the reverend mother acts like it's the first time she has heard it. In reality, she would have heard the rehearsals as the convent is very quiet and you can hear the choir rehearsing when she tells Deloris she will join the choir.
Suggested correction: She may have heard it, but never seen it. What startled her were the moves.
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.
Other mistake: When Mary Clarence enters the choir room the first time, Mary Lazarus approaches and asks only if she's a soprano or alto, when there are lower voiced baritones and bass nuns in the group.
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.
Suggested correction: The only genuine mistake is that Doloris wouldn't see Vince looking at Ernie or Joey but as the office door is glass, she would be able to hear them talking. Example being when Deloris leaves and is standing outside with the door closed she can hear Vince telling Willy and Joey to bring her back for a talk or, if she runs, to "take care of it".
Except that she never stood outside the door listening to the entire exchange. As soon as she got to Vince's door, she didn't stop to listen to the entire meeting she immediately opened the door, walked in and witnessed the murder and nothing else. Plus, about five seconds after Vince says, "Say, goodnight, Ernie", is when Delores arrives.
To add, the only way for her to witness the entire exchange between Vince and Ernie was if she was standing in the room the entire time which she wasn't.