Plot hole: It has already been mentioned that a certain shot reveals that Sidney isn't wearing the bullet-proof vest when she should be. Further to this, most of the shots in the climax sequence make it impossible for her to be wearing one, as you can see the contours of her chest throughout. A bullet-proof vest would flatten the appearance of this.
Plot hole: Why would Madison Lee put the bomb in the car if she was so convinced that the Angels were dead? If she wanted to off them just in case, she could have shot them while they were unconscious. (01:21:50)
Plot hole: In multiple scenes in the movie the starship is in a gentle rotation which allows 1G gravity on the ship. When the power to the propellant is cut the rotation stops and gravity is lost. Such a design for a starship doesn't make sense as the entire structure could be put in a continuous motion, as is indeed done with many probes today without requiring the continuous addition of power. Even if this design was chosen with part of the structure fixed and party of it moving around it still seems unlikely that the rotating part would come to a grinding halt within seconds (if it did, the friction of the structure would be huge, requiring enormous levels of energy to keep it moving) The only reason the movie chooses this unlikely design is to integrate the crucial shot of Aurora floating out of the pool when power is first lost.
Plot hole: The secret CIA base at Kamp Woody was underground. Kids searching for years have combed the camp, but never found it, but when Cody is going down the escalator, you can see bright skylights on the roof. If the sun is able to shine through, that means the skylights aren't hidden, and the kids would be able to find the camp.
Plot hole: Jamiel delivers Ali Baba's ransom note to Hulagu Khan by throwing a knife, and the shocked Khan and his guards look to the window. Since Jamiel does not duck away immediately, he should have been seen and identified immediately, but nothing of that sort happens.
Plot hole: Alain joins the Legion, goes through extensive training and eventually gets his photograph taken. That's how Galgani recognises him and sends two men to kill him. They arrive with a platoon at the fort just after Alain, Mackintosh and Luther. The photograph would have taken a while to get back to France and then the two men would have to go through the same training. So how do they both end up in the same fortress after they joined the legion long after Alain?
Plot hole: In the Banker's Office, Bond takes the strap from one of the window blinds to facilitate his escape. Overlooking the large quantity of cable he ties round the belt of the villain and his own belt, there must be an awful lot of strap for one blind to allow him to drop from that high up to the ground (well over 50ft?).
Plot hole: In the end of the movie, when Willy Wonka decides to visit his father, his father does not recognize him until he looks at his "rare teeth." But the wall of newspaper printings that Charlie was looking at included a recent enough picture of Willy that the father would have definitely recognized him, before seeing his teeth, as Willy doesn't look like a normal person with that outfit.
Plot hole: When Wolf and Tony find Virginia in the Huntsman's tree house, she tells them that he chained her up, so she can't go downstairs and open the door from the inside. However, after Wolf climbs her hair and enters through the window, the two of them walk down the stairs without any chains stopping her. They couldn't have cut her free with the magic ax because Tony was holding it, and he was downstairs by the door.
Plot hole: There's no visible evidence that Team Rocket has taken away Ash, Misty, and Brock's Poké Balls when the gang was in the cage, so why don't the Trainers call out their Pokémon (Brock's Onix would've helped out very much) and escape the cage?
Plot hole: When the two Legionnaires open the gate of the Hadrian's Wall, they lean forward with their shoulders against the doors as if to push, but they are really pulling. (00:33:10)
Plot hole: When Fogg convinces the cargo ship captain to take him to Shanghai, he pays for the passage of himself and two of his colleagues. One of these colleagues is Aouda, but as Passpartout is not there, the other one must be Fix. Why, then, does Fix have to pay for his own passage? If you notice, Fogg seems surprised to see Fix on board.