Continuity mistake: When Julie talks to Courtney at lunch, she's wearing a headband and the ends of her hair are flipped out. When she's waiting for the bus, the ends of her hair are curled under. Later on in the scene her ends are flipped out again.
Continuity mistake: At the end when it is revealed that Courtney killed Liz, we see several of the teenagers standing right in front of the stage. As Courtney walks through the crowd several of the teenagers have moved away from the stage and further back in the crowd. They couldn't have moved that fast through the rest of the crowd.
Plot hole: The whole point of the deception is that Fern Mayo, the geek, turns overnight into Vylett. No one at school has a clue about her real identity till Marcia and Courtney put up posters. So this deception carries on for several weeks before the two girls expose it. There is no way this would work. A school will not simply accept a new student without bothering to register her, yet when Fern Mayo just doesn't turn up to school one day, and Vylett does indeed, none of the teachers find this strange, or bother enrolling "Vylett" officially in school.
Continuity mistake: When Courtney, Fern and Foxy are in the cafeteria and they're all drinking diet Coke, Fern has her Coke in her hand near her face when Courtney names her Vylett, but when the shot changes to Fern's face, the Coke is on the table. When the shot changes to show all three, the Coke is in Fern's hand again.
Continuity mistake: When the three girls are carrying Liz's body into the house, she is all paled and bruised. When the camera shows her through different scenes the bruises on her body appear, disappear and reappear through scenes.
Other mistake: Given the three girls are in tight skirts and high heels it seems unlikely they could've caught up to Fern who's wearing a loose skirt and loafers.
Answer: The band had recently broken up when Jawbreaker was released, so maybe that had something to do with it. Or maybe just a good old-fashioned disagreement about how much VS would be paid for using their song? I agree, the soundtrack seemed somehow empty without it.