Plot hole: They all drop their backpacks and bags 3/4 mile down into the hole before climbing by rope into the caverns to begin their journey. Later in the movie, they are all sitting deep in the caverns complaining about the lack of water supply. Suddenly the long-haired guy pulls out a large glass bottle of gin, completely intact and they all drink from it. There is no way his pack could have fallen 3/4 mile onto a hard surface without that bottle breaking.
Plot hole: Granted, Coffee is suffering from "high-pressure nervous syndrome," but if you're a Navy SEAL, wouldn't you notice whether or not your pistol has a magazine in it? Monk pulls the clip out of his jacket and starts knocking rounds out of it for the rig crew's benefit; the same dramatic effect could have been achieved with a handful of cartridges he could let slip through his fingers. You could argue that Monk didn't have enough time to unload the gun and replace the magazine, but in that case, I think the scene where Monk briefly had the gun should have been a bit longer. (Even had the empty magazine been IN the gun, Coffee still might notice the difference in weight, but that would be easier to suspend your disbelief for.) (01:43:53)
Plot hole: When Captain Towers gives his XO an injection to allow him to die in peace, he, properly, swabs the site with alcohol, and slips the needle into the vein. However, immediately below the injection site, is a hep-lock.a port installed into a vein to allow injectables to be administered. I cannot imagine that a senior Naval officer would be so ignorant of the port's function.
Plot hole: When Gallagher is trying to kill the senator at the end, he is fired on by his bodyguards. Yet when they finally catch up with him, they're quite content to stand back and watch him torch the senator. One of them even lowers his gun. They couldn't have known Gallagher and the senator were aliens. (01:27:20)
Plot hole: The creature gets caught in the fishing net and (after a struggle that shook the whole boat) freed itself. The scientists, upon drawing up the net, find one of the creature's claws, and thus they now seek its source. Shortly after, while Mark is busy loading a harpoon gun, Dave is protesting, stating, "This...this thing *alive* and in it's natural habitat..." It would seem that at this point, they know the creature is *not* dead, but very much alive. They dive, they see it, Mark shoots it with a harpoon, and then upon surfacing, they argue a bit before reporting what they saw to everyone else. So why after seeing it underwater, fully knowing that "this thing (is) alive," do they act so surprised to see it, as if they didn't have a clue it could possibly still exist?
Plot hole: Whilst on the surface a drifting ship is seen and an officer and two sailors are sent to check it. On deck the officer says check fore and aft. The sailor who goes to the right and out of sight is back in 5 seconds. This is not enough time to check his allocated section. The script should have shown the officer check his watch (dial visible) and say something like "you have got 15 minutes". Next shot to show the officer checking his watch again and we see 10 minutes have passed and the men return.
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: There are two timelines in the X-Men franchise - the original films and the prequels, up until Days of Future past, which alters the future, and at the end reveals that Jean Grey, Professor X and Cyclops are all alive, rather than dying as they did in X-Men 3. The "new" timeline is then followed in Apocalypse and this movie, giving them a bit of leeway to make changes, much like the new Star Trek movies. Only problem is...Jean Grey dies in this movie! So no way her older self can be around in DoFP.
Plot hole: One alien egg is shown hanging from the wall at the start of this film, yet there's no way it can be there. The queen didn't take any with her from LV426 in 'Aliens', and if she did, she had no opportunity to place them on the Sulaco between exiting the dropship's landing gear, engaging Ripley and being killed.
Plot hole: Considering that this family has been training for the mission for years and certainly have received some instruction in astrobiology, they are awfully carefree around the cute little alien. Any real space farer would be aware of the enormous potential problems with first contact, like incompatible biochemistry (aliens might exude deadly toxins from their skin, be eaten alive by human-exhaled oxygen, etc). They even feed it human food without analyzing the alien; again, this could kill it, make it chemically dependent, cause it to go into a mating cycle, etc. But it's cute alien, so naturally they don't worry about any of this.
Plot hole: There is no way that 'coast of Iceland' could ever have been mistranslated as 'coast of Ireland'. For this to have happened, they would have had to have thought that the 'C' rune was an 'R' rune, but they had already deciphered the word 'coast', so they knew what the 'C' rune was. The 'O's are the same rune and the 'A's are the same rune, plus there is one rune for every letter, so it it's a direct letter-by-letter translation.
Plot hole: Dan returns from the future with a vial of toxins with him that can kill all the white spikes. He tells somebody to start mass-producing it but this information is not spread across governments or even made public, but it is the one thing they have that can prevent humanity's extinction and making people aware of that will stop the rioting.
Plot hole: How would any of the EVA/16MM video footage be recovered in the first place? Astronauts took pictures like these on rolls of film, and those were developed well after the end of the flight. If the spacecraft had not been recovered at all, then the footage would simply be a piece of orbiting space junk. (01:22:40)
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: Even if the 30 bus passengers that were already dead had been burned up in the explosion of the building their bodies would still have been autopsied after the fact, thus proving that Phoenix had killed them beforehand and vindicated Spartan.
Plot hole: Brent discovers that Taylor is on the planet and has a connection to Nova through the dog tags she is wearing. However, throughout the first movie, Taylor never had any dog tags on his person. Also, his ship was destroyed, and he only managed to retrieve a life raft and supplies. His belongings and clothing were taken from him when he was apprehended by the apes. Taylor should never have had any dog tags to give to Nova or for Brent to discover. (00:11:10)