Plot hole: When the cop is in the room and he realises how the teacher escaped from the hotel, he pictures him walking out in the bellboy uniform while the cop is downstairs. However at this time he should be upstairs with the girl in her room, because he is still in the room when she runs out of the room into the cop. For this to work out, the teacher would have to have left the room before the girl even got there.
Plot hole: Hoffman is able to implicate Agent Strahm as the mastermind behind the main series of traps in this film by planting Strahm's cell phone at the scene. However, Hoffman is repeatedly shown to be touching things at the scene without wearing gloves, so a forensics sweep of the crime scene afterwards would show Hoffman's fingerprints all over the place and reveal him to be the actual mastermind. Agent Erickson arrives at the crime scene before the two survivors of the traps complete their tests, so the forensics team would have been called in before Hoffman had a chance to remove any evidence that would incriminate himself. As a forensics officer himself, Hoffman should know better.
Plot hole: One of the flying dragons impacts the right outer engine of the B-29, and the fire spreads to the right inner engine. The crew lands the plane on the island, and the girls rebuild both engines, despite the fact there are no parts available on the island.
Plot hole: Zi Juan tells the rest of the group when they are in Shangri La that she will take the first watch at the entrance and guard against the emperor getting in. A few shots later, she then decides to have a conversation with her daughter nowhere near the entrance, and now with no-one guarding, means he gets in unchallenged.
Suggested correction: A character briefly leaving their watch to deliver important information as Zi Juan was doing isn't a mistake, and it's definitely not a plot hole, since it in no way contradicts the movie's logic or creates a hole in the narrative. At best, Zi Juan was being a little foolish leaving her watch, but a character being a little foolish isn't a "movie mistake." After all, people make foolish choices all the time in real life. Plus, as demonstrated by the movie, it doesn't really matter anyways - the Emperor's powers are back, so she wouldn't have been able to stop him even if she had kept watch.
Plot hole: At the end of the movie we discover that the main character (Claire) was in the plane crash and was sitting next to Eric as the plane started to go down. However at the beginning of the movie( before we are supposed to know Claire was in the crash) Eric can be seen but Claire is not next to him. (00:01:10 - 01:19:20)
Plot hole: Ami's arm was sliced off, and the wound went untreated (you can tell it was not cauterized in later scenes) for a number of hours before it was stitched up. All this time, we see her loosing ludicrous amounts of blood. Yet, Miki looses her foot, and dies of blood loss only a few minutes later, despite her wound and blood loss being much less severe than Ami's. An inconsistency in the style done solely for dramatic purposes.
Plot hole: After Eli's guardian is hospitalised for acid-burning his face, Eli hears on the radio that they can't ID him because of his facial wounds. When we see him in the hospital however, only half his face is injured, the other half is fine which would make a mirror composite easy for lab techs.