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: This observation regards a computer whose memory architecture is on a physical scale (e.g., size) that allows multiple humans to enter and maneuver within it. With electronic components, scale imposes a design limitation such that the greater the distance between components, the more time is required for a signal to traverse between components. This computer's massive size would assure substantial performance limitations which are inconsistent with the plot line of the computer's overall power.