Early in the movie, during the frat party, Veronica throws her burning glass out the window and it lands in a trash bin that sets on fire. When she leaves the house, the fiery trash bin is not under a window.
After JD blew 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, & lower than it was in the previous shot.
When talking about the Lunchtime Poll question, Heather Chandler tells her friends she had just come up with it in study hall. However, when Veronica asks if it is what Heather Chandler was talking to her on the phone about the night before, Heather says yes.
When Heather C is setting up her backswing with the croquet mallet, the positioning of Heather M behind her alternates between close and far back, depending on whether the shot shows their feet or upper bodies.
After exiting the restroom and entering the cafeteria, Heather #1 is holding the red lunch poll clipboard. Heather #1 is still holding it when Veronica starts walking towards JD (and you can see both Veronica's hands are empty), but when Veronica arrives and asks JD the question, Veronica magically has the clipboard.
When Veronica and JD are waking up in the school parking lot, Veronica holds her left arm carefully. When she takes the lighter and puts it on the palm of her left hand, it is obvious that this is not a real hand.
When Veronica comes out of the Snappy Snack Shack with the large Slushee that JD just bought for her, she waves it around and holds it with a bent wrist in a way she couldn't possibly do if it were almost full of a heavy liquid (revealing that the cup is actually empty).
When Veronica fakes hanging herself in her bedroom, she's suspended between her bed and the fireplace when J.D. comes in the room, but when she unties her sheet harness she falls onto her bed. She should have fallen on the floor in front of the fireplace.
The whole boiler room sequence - cut with the footage of the pep rally - takes much more than the time which is set on the bomb, which is about 2:15. At 1:40 and ticking down, both fight for the possession of the gun and JD kisses Veronica. When she repossesses the gun, she walks by the bomb and it says :57 seconds. When Veronica is pointing the gun at Jason, you can see that there are 42 seconds until the bomb blows up. But, when she asks him how to stop it a few seconds later, it is still on 42 seconds. They have a conversation which lasts about one minute, yet the clock advances only 12 seconds to :30 seconds. However, the final 30 seconds takes about that much screen time.
When J.D walks out of the school after the final boiler room incident, we see him walk a short distance away from Veronica so he can blow himself up. But in the next shot, Veronica is higher up on the steps and J.D is much farther away from her than he should be.
Near the end, when Veronica & J.D. fight, the blood on Veronica's face changes from scene to scene. This happens again immediately after J.D blows himself up, and Veronica is walking down the school hallway.
When Veronica is holding the gun on JD in the boiler room, its position changes between shots. When looking over JD's shoulder at Veronica, the gun is aimed at his head. When looking over Veronica's shoulder at JD, the gun is aimed at his heart.
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.
(at around 1h 17 mins) Veronica lies on her bed and the alarm clock on the nightstand reads about 6:59. Later, JD sneaks into the bedroom, but when he arrives, the clock clearly reads 6:55. This turns out to have been a dream, but the dream offers no explanation for why the clock turned back 4 minutes.
When JD shoots Ram, he shoots him in the throat. Ram has a bullet wound in his throat when Veronica is kneeling beside him. Then when the cop finds him, the bullet wound is now in the middle of his chest, he has blood coming out of his mouth, and his throat is unharmed.
Right after Heather Duke and Heather McNamara drop in on Veronica and Betty Finn playing croquet, Veronica talks to her parents about the suicides. She still has a croquet mallet in her hand, so little time can have passed. Heather Duke rushes in with a shopping bag, and tells Veronica that while at the mall they heard about Martha Dumptruck's suicide attempt. But Heather Duke had just left Veronica's house - there wasn't enough time for these events to happen.
In the cafeteria scene when J.D. fires the gun at Kurt and Ram, a burn mark from the powder blast of the blank that is fired from the gun can be seen on a clear protective barrier that was between the gun and the camera. When viewed in real time, it looks somewhat like a projectile that came out of the barrel of the gun, but a stop-frame or slow motion viewing shows that it is a stationary spot that never moves after it first appears.