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: 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: When Grug is trying to escape from the explosion behind him he sees Douglas and says "Douglas! Hey I know that guy!" This is not possible since he neither knew the name of the creature or was nowhere around when Douglas was with Thunk.
Suggested correction: Thunk might have told him who Douglas is.
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: 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: During the final scare event, Mike gets a perfect score because Sully broke the simulator to allow the 6th scarer to get a perfect score no matter what. After the contest, the simulation resets and Mike pretends to scare the child in the simulator and it registers a perfect score on the scoreboard for the 6th scarer when it should really have registered a score for the 1st scarer, because the simulator had been reset.