Plot hole: When the group is walking through the jungle for the 2nd time, they have nothing more than their backpacks and a horse to accompany them. Suddenly we see them rowing down a river on a boat and raft. After making peace with the savages, when they have to let a group member go to get medical help, they have been washed ashore as they have been traveling on a single raft since the canoe was damaged by spear attack. How is it that they had a horse and an Indian guide to send away with their injured man? (01:16:55)
Plot hole: In multiple scenes in the movie the starship is in a gentle rotation which allows 1G gravity on the ship. When the power to the propellant is cut the rotation stops and gravity is lost. Such a design for a starship doesn't make sense as the entire structure could be put in a continuous motion, as is indeed done with many probes today without requiring the continuous addition of power. Even if this design was chosen with part of the structure fixed and party of it moving around it still seems unlikely that the rotating part would come to a grinding halt within seconds (if it did, the friction of the structure would be huge, requiring enormous levels of energy to keep it moving) The only reason the movie chooses this unlikely design is to integrate the crucial shot of Aurora floating out of the pool when power is first lost.
Plot hole: After escaping from execution, the assassins still made use of throwing knives out of their garments as they ran through the city. These would have been removed from them before they were shackled in the cell.
Plot hole: When the dome of crystal collapses, all the animals inside immediately grow old, including Brook, implying that the magic from the crystals is completely gone. However, when a tiny piece of crystal lands in the hot spring, it creates a 'fountain of youth' which the animals then bathe in to regain their youth. If that little piece of crystal worked, then why didn't the many crystals from the broken dome still work? Also, how is Brook able to leave the fountain of youth and go looking for Sid at the end of the movie without growing old?
Plot hole: The Chinese army displays a great variety of (often anachronistic) weapons and they spent considerable resources arming and reinforcing the Great Wall to challenge the beasts who have been plaguing their land every 60 years for thousands of years. but despite having records of magnets being effective against them, with magnets being well known to them for centuries (early magnetic compasses were available in the IV century BC, and the movie is set in the XI century) they made no use of that at all.
Plot hole: In this film the aliens are said to be operating with a hive mind, and are all telepathically linked to the alien queen on the mothership. It is also stated the mothership from the first film also had a queen that was never seen. If that is the case, then there would not have been any need in the first film to use Earth's satellites to coordinate the attack.
Plot hole: When Norm is stuck under the satellite tower after disposing of the condos, he has flashbacks to numerous moments earlier on in the movie. One of the flashbacks is of Socrates saluting Norm, but the moment where Socrates salutes Norm did not occur until he was on the cargo ship being shipped off to New York and was something that he did not see Socrates do; there would be no way for Norm to have this flashback. (01:18:00)
Plot hole: Durotan's clan is the Frostwolf clan, orcs who ride big white wolves. The problem is...they are riding those wolves when they are in the human world, but those huge wolves made to be orc mounts were not with them when they crossed the portal from their homeworld. Unless the human world has the same wolves and they managed to tame them in record time, it's inexplicable.
Plot hole: At the end, Jake utilizes multiple Loops to reach September 4th, 1943, the date from which Miss Peregrine's children impossibly entered another Loop set in the winter at the beginning of 2016. The closest date prior to this was in 1942, from when Jake waits for September 4th 1943 to arrive. However, having entered a Loop in 1942, he would have been unable to reach 1943 because he'd be stuck living the same day in 1942 over and over.