Plot hole: The fact that a five minute timer starts after the three Cerberus codes are entered defeats the purpose of the program. If they program was made to destroy their own nuke warheads in case of a misfire you would expect them to be destroyed as soon as all three codes are in. (01:38:20)
Plot hole: The most secure prison in the world, designed with the advanced schematics of world leading prison-building architect (J.D Ray Breslin) has cameras somehow interconnected to one another so tightly that physically neutralizing one puts every other camera out of commission as well.
Plot hole: The Kaiju's EMP fries all electrical circuits next to him, and affects the base as well. If that's true, how did the helicopters carrying Gypsy survive the blast without having their electronics fried? EMP pulses induce current in all electronics regardless of whether they're powered on or not. (01:18:00)
Plot hole: Even if someone would make all nuclear powers launch their nuclear missiles and then destroy them you still wouldn't have a nuclear weapons free world as most of those nations have plenty of nuclear weapons in reserve. A lot would be even be armed and ready to go for a possible second strike. (01:24:10)
Plot hole: They discover a "not so well hidden" microphone in the car that tells them the "man" is listening to them, but it is ignored throughout the rest of the movie, especially when setting up a video loop to cover their extracurricular activities. (00:30:00)
Plot hole: How come the Extremis serum was able to regenerate Ellen Brandt's arm but not repair the scar on her face? According to the movie, the serum is supposed to rewrite the body's genetic code and constantly repair damaged cells, so her face should have been restored to its original state, just like her missing arm. Even if she had been born with the scar the serum would have healed it, just like it healed all of Aldrich Killian's physical impairments. (00:51:40)
Plot hole: After Reverse Flash saves Lois Lane and kills all the Amazons that were attacking her, he disappears, just before a group of resistance fighters shows up. They know that they didn't take out any of the Amazons, it's obvious that Lois didn't kill them, yet the resistance members show no concern as to who was responsible. The war involves three separate groups, the resistance, the Amazons and the Atlanteans, each of whom is equally hostile to the other two. As such, the resistance cannot assume that whoever killed the Amazons must be an ally and let their guard down, as it could easily have been an Atlantean force, who would make no distinction between the Amazons and the resistance and would attack them on sight. An experienced resistance team would not be so casual about the situation. (00:40:50)
Plot hole: According to the flight recording, Odyssey was on an uncontrolled pull towards the Tet as Jack says, "We're not getting away from this thing." So even if Jack jettisoned the sleep module where Julia was in, the module should not be able to get away as the whole ship is being pulled towards the Tet.
Suggested correction: It can be assumed that the jettisoned module has enough "jettison power" to force it away from the command pod. And in turn that force would move the pod further towards the Tet. It's reasonable to assume the Tet couldn't pull the module that was moving away, under dramatic force, and to which it didn't have line of sight (which was blocked by the pod).
Plot hole: During the warp-speed chase, the Vengeance literally blasts the Enterprise to pieces, and dozens if not scores of Enterprise crew members are killed and injured in the carnage. The medical crew, including Chief Medical Officer McCoy, should have been working feverishly on the wounded and dying for hours, at least. Instead, as Kirk asks Khan for help, the Sickbay is practically deserted, and McCoy is almost idly conducting blood experiments on a dead tribble. There's no sense of a catastrophic medical emergency whatsoever. It's as though the Sickbay sequence was shot for a different script in which there was no emergency, and then lazily inserted into a rewritten script.
Plot hole: After blowing up the gate, the President turns on the TV news in the car...for no reason, other than for them to conveniently get the information that Channing Tatum's daughter is about to be executed, distracting him.
Plot hole: The same zombie who can smell through a vault that Gerry is not worth a bite, just minutes before couldn't smell the presence of three alive humans two meters apart.
Plot hole: Nick Fury wants to detain Tony as he is the only witness. Tony takes off and Nick Fury even says to apprehend him so their only witness isn't killed. Yet when the S.H.I.E.L.D. robots confront Tony at Pepper's vacation spot, they say they are authorized to use deadly force against Tony. And Nick Fury even orders them to fire when Tony resists. If they need Tony to keep their only witness alive, why try to kill him when he doesn't cooperate? (00:31:05)
Plot hole: At the end of the film Shaw and Dom drive their cars onto the plane and the pilot says they are too heavy to take off, but Shaw's team consisted of an extra car, which the plane was clearly prepared to take off with.
Plot hole: Every single one of the ronin are portrayed as being extremely lax with their most prized possession, their swords. When they first gather, one of the ronin tells Oishi "We do not have any swords", whereupon Oishi casually hand over his own. First of all, only the most poverty-stricken and desperate ronin sold their swords, as giving up one's sword was the ultimate humiliation for a samurai, it was a denial of both one's status and legacy. Secondly, selling your sword would mean never being able to be employed as samurai again, or even to be hired as a temporary bodyguard. Thirdly, swords were often inherited from one's father, or given as personal gifts by parents or lords, not something one would willingly give up. It is possible a few of the ronin would have been driven to selling or otherwise losing their swords, but not every single one of the 50+ ronin who gather. And those who still had them would be extremely loathe to even lend them to others.
Plot hole: The robot pilots have no screens/monitors in the robots to show them what's outside - only some obviously unimportant text or graphics. How could they fight the monsters without being able to see what's in front of them (or anywhere else, for that matter)?
Plot hole: Luka sneaks into Bayonetta's hotel room and plants a hidden microphone. While sneaking out, he is caught. That's when he is astonished to find a child with Bayonetta who calls her "mummy." He does eventually escape the room and sits in corner with his radio, surprised that they both went to bed and he receives nothing. The problem is: One must be an idiot to plant a mic in a lone woman's hotel room in the dead of the night, unless he truly enjoys listening to her snoring! Planting the mic in her apartment or office, or on her mobile phone makes a lot more sense.
