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.
Suggested correction: This is not necessarily inconsistent with the movie's time travel logic. Since Tim goes back in time to visit his father and inside that particular time travel, they use time travel to go back to a day where Tim was a child. Then, they return back to the original time travel where they're playing ping pong. At that moment, both of Tim's kids were already born. So, when he returns from the ping pong scene, there's no change regarding his kids.
Also, paraphrasing the Dad, he said they aren't going to change anything. It is more like reliving a memory than changing the future to get what you want. The Dad couldn't go back to not smoke before his kids were born because that was major and would have changed the course of his life; walking a bit differently on a secluded beach that you walked on in your younger days (as long as you spent the same amount of time - presumably) would not alter the trajectory of one's life.
The slightest change in 1 second of being on the beach would absolutely affect his kids. A man produces 1500 new sperm every minute. Altering the timeline and delaying every event that is going to happen by literally 1 second would most definitely alter which exact sperm was used when conceiving both of his first two children.
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: 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: 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: 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: 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.