Plot hole: When Tim takes his sister Kit Kat back in time, she gets a sudden brain change as she realises she's now going out with his friend and finds him attractive in the changed timeline. However, Tim has no idea anything's different in his life until he gets home and discovers his daughter has become a son.
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: 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: Gerry's wife uses a rocket boot to break through a window and then slides down a curved wall to get to their son. She does so gracefully and takes off running. Gerry slides and takes a hard tumble and rolls down, landing on the ground. The next shot shows Gerry running behind his wife and not too far away as they reach their son. Even if it was to show a little time passing, there was not enough distance between where they broke the window and their son for Gerry to have picked himself up and catch up to his wife before reaching their son, especially with his wife being a worried mom doing a full on sprint to her kid.
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: 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: 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: When the robot pilots first connect after the first attack, Red tells the story of his battle. They don't seem to even notice the dozen or so civilian bodies they have to actually physically step over - and the bodies are just lying there along the sidewalk & parking lot; no signs of any monster attack, so how did they die?
Plot hole: If Chester's plan was to steal the machine the entire time why didn't he just have his people steal the machine while it was still floating in the air during the first film? There was plenty of time to capture it before the food started mutating so what was he waiting for if he needed it so bad?
Suggested correction: Because he wasn't there in the first film? He first made an appearance in this film, doesn't know how to work the machine without Flint, and how the hell would he even get it in the sky? He also didn't even know about it, or what happened to Chew and Swallow, again, until he made an appearance in this film. Not a mistake.