Deliberate mistake: When the girls all order their food at the drive through they get their food but never pay. (00:17:15)
Deliberate mistake: In Paris' death scene, he blows alcohol onto his torch that illuminates the creatures around him. However the area is still illuminated after the light from his torch has disappeared. (01:12:05)
Deliberate mistake: When Leonard snaps a picture of Jimmy's body his head is lying between his shoulders looking straight up, but in the polaroid his head is lying to the right, and it is, in fact, a different actor altogether. (01:39:10)
Deliberate mistake: Elizabeth Shue uses a drawer handle as an electromagnet. OK if it's really a magnetic material but lab furniture is generally made of aluminium or stainless steel which is not. There is no way that they would use an iron handle in a potentially wet, and hence corrosive, environment such as a freezer.
Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.
Deliberate mistake: When Alex is in the cabin opening the can the pull tab is already lifted up making it easier to open because he is wearing gloves. It was already up when he took the wrapper off.
Deliberate mistake: Some of the text in this movie is in English, but some is in Japanese. Most noticeable when Tai writes the letter to Sora.
Deliberate mistake: In chapter 15 "Bad Service" as Kim drives away and almost hits the kids which are supposed to represent the "Burkittsville 7", count them. There are three girls and four boys. Rustin Parr kidnapped 8 kids; 4 boys and 4 girls. Kyle Brody survived so the Burkittsville 7 should be 4 girls and 3 boys.
Deliberate mistake: When Carlo and Bonehead go upstairs to confront Jack at the hotel, Bonehead accidentally shoots Carlo in the leg and Carlo fires eight shots in retaliation at Bonehead killing him. Carlo immediately bursts into Jack's room same gun drawn. When Jack jumps out the window Carlo begins firing and shoots another 15 times. There is no way the single clip in the gun Carlo uses could possibly fire 23 rounds.
Deliberate mistake: In the scene with all the coffins and new Skull "recruits", Lucas knocks on the unopened coffin and Caleb pops up. The next shot is a wider shot that shows everyone standing around Caleb's coffin, but the guy in the coffin is not the actor playing Caleb, but a stand-in.