At the beginning of the movie, when the bus is shown en route to the train station, the hubs of the wheels are dirty silver but in the next shot, when the buss is pulling in to the train station, the hubs are black. Not only that, but it is not the same train station in the second shot as in the first shot.
When Mary was striking Marvel-Ann's mask with a mallet, she was obviously missing the mask. Also, the mask never moved, with every strike.
During the victim/rescuer swim test, both of the girls could not swim and thus were drowning. Sister Clarissa jumped into the pool and grabbed Mary with her left hand but could not reach Rachel. So Rachel swam to her so Sister Clarissa could rescue her.
Vicky Albright, who played Charlotte, was wearing her engagement ring, on her left hand, in the art room scene. The one where the art teacher's hand was accidentally painted by Rachel. She did not wear a ring in all of the other scenes.
When Mary and Rachel were in the bathroom, Rachel was holding two cigarettes. Mary lit one of the cigarettes but not the other, because it was all ready lit. For that matter, it had been lit for awhile. Rachel was simply holding the cigarette that Mary had already been smoking while Mary got her lighter to light another for Rachel.
There is no way that a couple of cigars could produce enough smoke, coming out of the window, to simulate a real fire. Also, with the small amount of smoke coming out. If would only take a fire extinguisher, or a couple of buckets of water, to put it out. Also, nobody bothered to check the room to see if anyone was in the room.
While the band was rehearsing and finished their song, Rachel hit her cymbals about a half a second late causing the girls to turn around and stare at her. The problem is that about four of the girls turned around to stare at her before she hit her cymbals.
In fact, they turned to stare at Mary who struck the bass drum first but also late.
When Rachel knocks over the bust in the art room, there is already debris on the floor from something else (probably another bust used in a take) and when Rachel goes to pick up the pieces of the newly broken bust, she picks up the stuff that was already there.
Mary wakes up and noticed that it was 8 am. The clock was not working. Either it was not plugged in or disabled. The second hand was stuck on the 4 and did not move.
There were two scenes where the girls were washing dishes. The scene after being caught on the slide and the scene after Marvel-Ann was rescued from the plaster mold. In both dish washing scenes, the dishes and pots were stacked exactly the same. Obviously the studio saved time and money shooting one shot for both scenes.
As an addendum to the previous comment about the appearance change in the school bus' wheel hubs, Sister Clarissa even makes reference to them, saying to the conductor, in effect that "we got a new paint job." Oddly, the rims change back and forth several times within the movie. It's obvious that certain scenes were filmed out of sequence.
When Reverend Mother put the trophy on to the mantel and removed the balloons, you could see six to seven round studio lights reflecting off of the balloons.