Continuity mistake: During the lunchtime poll scene, just after the three Heathers and Veronica leave the bathroom in the canteen, Veronica does not have the clipboard with the poll on it. You see her stare at J.D and she still does not have it, but when she begins walking towards him, it appears in her hands.
Continuity mistake: After Heather drops dead from drinking the poison, her body changes position between shots. In the first shot of her body (an overhead shot) she is lying on her left side with her right hand curled under her chin. In the next shot her body has rolled to the right and her right hand has moved away from her body.
Continuity mistake: At the end of the movie, when JD is about to blow himself up in front of the school, JD and Veronica are talking in a normal tone of voice, and he seems to be standing only a few feet away from her, to her left. In the next shot, the camera pans a shot of the front of the school, and JD is right in front of Veronica, and 100 feet or more away from her.
Continuity mistake: When Veronica opens the locker of deceased Heather Chandler, there is a photograph taped inside of all three Heathers and Veronica. The photo shows the girls at Veronica's house, posed with their croquet mallets. They are wearing exactly the same clothes as they were during the croquet scene, and knowing these girls they would not wear the same outfits on the same day often. Which implies that it is supposed to be a photo taken from that day at Veronica's house. Now here's the mistake - how could a photo from that day be up in Heather's locker, when she died the next morning? The photo was taken on a Friday afternoon, and Heather never made it to school again.
Continuity mistake: In the scene after JD blows himself up, Veronica goes back inside the school where she runs into Heather Duke. Veronica then kisses Heather on her cheek, leaving a black mark on her face. In the next shot as Veronica walks away, Heather turns around and you can see that the black mark is darker, larger, and lower than it was in the previous shot.