Plot hole: The spinosaurus manages to smash through a metal reinforced wall designed to stop dinosaurs getting past it without too much effort, yet it can't get through a wooden gate secured by some metal bars. It makes no sense.
Plot hole: In the final showdown, when Bond is fighting with Stamper, the girl is wrapped in a chain hanging from a crane and dropped in the sea. After the boat blows to bits, the chain continues to hang down even though there's nothing holding it. It even keeps hanging after Bond's swum down to untie her. What's keeping it there? Do all stealth battleships come with buoyant chains? With both arms at least partially free, why doesn't she just climb back up the chain?
Plot hole: Bond makes a huge tactical error after diving to the St. Georges. He knows the Russians and their operatives are after the ATAC. The ATAC itself is expendable to Britain, since it has a self-destruct mechanism that under proper procedure would have been set off when the ship sank. So why is Bond trying to retrieve it? Because he disarms the self-destruct, he actually allows Kristatos to get his hands on it, forcing Bond to track it down again and, to stop the Russians from getting it, HE DESTROYS IT! So why doesn't Bond, instead of disarming the self destruct, set a timed charge or toss a grenade in the room to destroy the ATAC while it's at the bottom of the sea? The answer is, of course, that if Bond destroys the ATAC before the bad guys can get at it, the movie's over. Even so, at the end, when Bond finally does destroy the ATAC, he tells Gogol it's "detente. You don't have it. I don't have it." Clever line, but it reinforces the fact that the British don't need it. They can build another one.
Plot hole: Even if the white blood cells will attack and destroy the sub and the body of Doctor Martin the atoms would still remain and take normal size after the critical 1 hour is up. This would also apply to the laser gun which they forgot or left behind on purpose, as well as several dozen litres of saline solution which were miniaturised and pumped into Benes' body. He's in a lot of trouble.
Plot hole: In the Ice Tunnel scene, Manny, Sid, and Diego come to a stop on the vertical block of ice. It breaks, and they slide through a 'field' of icicles sticking out of the ground. Their 'sled' is shaved down to nothing, indicating that the icicles are sharp. After going through the same tunnel as the baby, how did the baby make it through that field? (00:46:53)
Plot hole: Even if boys of that age had the technical know-how to quickly repair Jeeps over 20 years old (seriously?), any gasoline in the tank would have long become unusable, the tires and lines would have rotted away, and the electrics would all be dead. Now if it was in the desert or a dry garage, it may have survived, but it's on a tropical island, in a shed that has all sorts of holes in the roof, leaving it exposed to every kind of weather the island could throw at it. In addition, the kids start the jeep with the small battery of an ATV, which cannot produce enough power to crank a Jeep engine.
Plot hole: In Paris, why does the assassin go to the ridiculous amount of trouble of swinging into the room on a rope with a machine gun when he came in from the lobby (as proved by the dead woman downstairs)? Alternatively, if his intention was always to surprise Bourne by coming in through the window, why venture downstairs at all? (00:44:07)
Plot hole: Hiding in a fridge (or anything else) in order to be conveniently blown out of the way by an exploding nuclear device is absurd beyond belief. The fridge is just so much extra reaction mass and would be vaporised by the expanding nuclear explosion - it wouldn't be daintily picked up and thrown a few kilometers to safety. If it was, why doesn't it land in a shower of similar artifacts which have also been dislodged and thrown around? Incidentally, even if it was thrown out of the way as shown, anyone inside it would be turned into a smear of strawberry jam by the acceleration required to beat the shock and heat wave of a nuclear blast, and then liquefied by the deceleration involved in hitting the ground at that speed.
Plot hole: In all scenes where special or heavy items are used against the sixers, they are 'zeroed' in waves or circles. This can be seen by their stations turning red in clusters. This makes no sense as the stations have fixed positions, meaning that the sixers would have identical positions in the Oasis and have no freedom or own will to move relative to each other.
Plot hole: Scar tells the pack he didn't make it to the gorge in time to help Mufasa. However Zazu was with them at at the gorge. He could have easily told Serabi or any of the other lions on the numerous times he spoke with them, exposing Scar.
Plot hole: After Superman has reversed time the Hoover Dam reverts to its previous undamaged state as it should, but Jimmy Olsen should then have been replaced back on the dam. Instead he interrupts the potential kiss between Lois and Superman and complains of being abandoned by Superman in the desert.
Plot hole: Blofeld tells the bad guys that they had Bond and let him get away. The woman says "but Bond is dead. It was in all the papers." As we saw in a paper near the start, there was a well publicised photo of Bond, and when she met him he wasn't using any kind of disguise, so how did she not recognise him if she'd seen the papers?
Plot hole: When April O'Neil calls Vernon Fenwick (drives the channel 6 van), he answers his phone and immediately says "O'Neil". When the scene cuts back to O'Neil, we see she called from a payphone. Fenwick would have no way to know it was her calling.
Plot hole: One of Snape's memories show Lily telling baby Harry to be safe, be strong. That had to have occurred before Voldemort killed Lily. Snape was not in the house until after Lily was killed and Voldemort was gone. Only Lily and Harry should have had that memory, but not Snape.
Plot hole: When Astrid gets on Toothless for the first time, Toothless takes off uncontrollably and tries to scare her. Hiccup seems to have no control over him at this time. How is that so if with the new tail fin, Toothless cannot fly without Hiccup's precise control of the tail fin? That whole sequence would have fallen apart. This mistake was even admitted to on the DVD commentary. (00:53:35)
Plot hole: How did the men on the ship get killed? The bridge was intact and the T-Rex was still inside the cargo hold. [A raptor was meant to escape from the boat when it pulled in to the harbour, but they cut the scene from the film and now that bit doesn't appear to make any sense.] (01:40:55)