Before the music competition, when the students are getting dressed, they appear to have on their school uniforms and/or white shirts. When they remove their robes just before they go on stage, they are wearing their colorful "street" clothes.
During the final performance of "Joyful, Joyful" Rita (Lauryn Hill) steps forward to sing. As the camera cuts to Ahmal (Ryan Toby) to show him step forward to sing you can briefly see Rita dancing with the choir just left of Ahmal.
Incorrectly regarded as a goof: Some of the "La La La" scenes in the new music room show the walls as having been painted, and the piano fixed, before the scenes in which the students paint the walls and fix the piano. However, as this is a montage, it isn't unreasonable for the individual scenes to be out of order.
Before the kids go out onto the stage to perform in the competition, Father Maurice speaks to them backstage. During that scene the kids' positions change several times, when they are shot to look like they are in the same position throughout the scene.
Sister Mary Roberts in the street concert scene is dancing in the middle of the stage, but when the next shot appears on screen she is on the other side singing into a microphone.
Although historically Roman Catholic Schools were staffed by clergy (i.e. nuns, priest, monks) by the early 1990's numbers in the membership of the clergy had fallen off. Thus it would be reasonable that Saint Francis would employee a fair name of lay teachers on their staff.
As Rita takes center stage to begin singing "Joyful, Joyful" she sees her mother come in and take a seat to watch. Because of this, she misses the first two piano intros to the song. As the third intro plays, Rita still shows no indication that she is going to sing, yet as soon as the third intro stops the girl behind Rita automatically raises her arms to begin signing as if she knew beforehand that it was going to take three intros before Rita would sing.
Before Sister Mary Clarence enters the music room for the first time, the students can be heard telling the same "Yo Mama" jokes through the door that they tell once she enters.
In one of the early shots of the choir's final number, the actress Jennifer Love Hewitt (position far right) is missing from the stage.
When Mary Lazarus is teaching a student a musical scale, she accidentally whacks herself with the baton. The baton's impact and the sound effect do not match.
In the final performance of Joyful, Joyful, as the camera crane hovers over the act then changes to a shot of Whoopi Goldberg conducting and dancing with the group you can clearly see a camera move into the dancers behind Whoopi before it cuts to the next shot.
Deloris's identity should have be been well known to Father Maurice and Mr. Crisp as well anyone else in San Francisco's Roman Catholic Diocese due to the fame she received during the first film. It's clear at the end of the first movie that Deloris received a lot of press and thus her identity should have been known.
Rita appears in a choir robe at the beginning of the climactic competition performance. However, the robes were most likely not purchased until after the fund-raising event, and Rita quit the choir before the fundraiser. As funds were tight, the choir would not have purchased extra robes, so Rita should not have had a robe available to her for the performance.
Sister Mary Clarence makes the boys remove their hats in class, but in the next shot Frankee and Ahman still have their hats on.