Factual error: KCN does not causes you to internally bleed, so Yuka Nakagawa wouldn't have spat up blood and died like that in the lighthouse, but would have rather died due to cessation of respiration.
Continuity mistake: In the first shot of Yuka Nakagawa as she covers her mouth after being poisoned with KCN by Yuko Sakaki, there is no blood on her hand as she has only just started to react to it. But in the closeup shot immediately afterwards there is blood already seeping through her fingers.
Continuity mistake: When Shuya Nanahara is being chased by Kazuo Kiriyama, Shuya shoots at Kiriyama twice, hitting Kiriyama in the chest and causing him to be knocked back a little, as he is wearing the bulletproof vest. However, when Kiriyama has Shuya cornered, there is no trace of a bullet hole.
Continuity mistake: When Kiriyama beheads Oda with Samurai sword, he is alerted to the noise in cottage where Kawaka, Noriko, and Nanahara are hiding. Inside the cottage, the trio see Kiriyama's blood-stained hand smearing the window. Then, Kiriyama hurls Oda's head, grenade in mouth, through the window and into the cottage. Despite Kiriyama's hand being soaked with blood, Oda's head is clean and spotless.
Audio problem: When Noriko tells Kawada that the food that he cooked was good, we hear him reply that his father was a cook, but if you watch him in the background you can clearly see he is just sitting there, and his mouth is not moving at all.
Revealing mistake: Many times throughout the movie, people are shot and they bleed, but their clothes don't have holes from where the bullets hit them. The most noticeable examples are when the teacher is shot at the end, and when the big gun fight between the girls breaks out in the lighthouse.
Other mistake: When Sugimura is looking for Kotohiki, he activates his scanner to see if she is nearby. The scanner shows her location, but fails to show either Mitsuko or Kiriyama, who show up quickly after.
Continuity mistake: After Kawada gets his bag, he realizes something and returns to the classroom. Tossing the bag back to the soldier who threw it at him, he points to a bag behind him on the cart and tells Kitano, 'That's my bag.' In the next shot, he is pointing to a bag in front of him.
Audio problem: When Chigusa attacks Niida after he shoots her with an arrow in the cheek accidentally, she stabs him in the back, they fall and roll to the floor, and then he tries to escape from her and begins ro run away, but she grabs him and screams "Bastard!!" However her mouth is completely shut.
Continuity mistake: After Utsumi dies, her right leg is bent upwards and falls down onto her left leg. When Shuya finds her dead, both of her legs are straight.
Plot hole: After Nanahara and Noriko run away from Akamatsu at the school, Niida shows up from behind some bushes opposite the school and inadvertently kills Akamatsu with his crossbow. But Niida is Boy 16, which means he should still be in the school building (he's supposed to come out after Noriko, who's Girl 15). There's no way he has any time to get into those bushes.
Continuity mistake: When Yuka Nakagawa is poisoned, her face lands in the bowl of poisoned spaghetti. A little later as the girls begin shooting each other, her face is now out of the bowl, and on the table instead. There was no movement to suggest that her face fell out of the bowl, as it quite clearly happens between shots (just before the girl jumps ono the table.)
Continuity mistake: In the initiation scene, Kitano kills Fujiyoushi by throwing a knife at her head. The knife penetrates her skull almost in between her eyebrows. Yet when he pulls the knife out, it looks as if the knife actually struck her under the eye or on the cheek. [And although this may have been corrected in some versions, it still exists in some versions and can therefore still be mentioned as a valid mistake.]
Continuity mistake: When Shuya finds Utsumi dead, the proximity of her head to the girl behind her changes between shots, as does the position of her tie and gun beside her.