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: Lucy jumps from the airliner and flies her hang-glider straight to Eduardo/El Macho's Cinco de Mayo party to find Gru. How did she know Gru would be there? He had no intention of going and only did so after he was pestered into it by the girls on the very night of the party, so he couldn't have told her himself. Shouldn't she have gone to his house instead? (01:09:50)
Plot hole: Each of the four magicians are given a tarot card that has a date (March 29), a time (4:44pm), an address (45 East Evan St), and a city (NY). When they enter the building on that date, they know which apartment to go to. The problem with this is that it was never stated on any of the cards which apartment to go to once they reached 45 East Evan Street. (00:08:40 - 00:10:05)
Plot hole: They aren't able to travel before the birth of their children or their children become different. Despite that, he visits his father one last time before their third child is born. His Dad and he then travel back to when he was a kid, which would have changed his first 2 kids.
Plot hole: When Jake first meets Reggie, he tells Reggie that the Great Turkey told him everything about him. Later in the movie, when Reggie goes back in time and introduces himself as the Great Turkey to a young Jake, he only tells Jake to find the "Pardoned Turkey" but never said that the pardoned turkey's name was Reggie, so there's no way the adult Jake would know Reggie's name when they first meet.
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: The premise of the movie is that a group of this man's genetic offspring have united to learn his identity. He receives a stack of the bios of those in the lawsuit. One of the children he visits is severely disabled in a nursing facility and would not have been capable of joining the lawsuit.
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: When Chucky is decapitated, no blood comes out. He still has the scars from Bride/Seed of Chucky so that means he's still in the same doll's body. The longer he remains inside the doll the more human he becomes, so he should definitely bleed by this point in time.
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.
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.