Plot hole: How can Bumblebee and Optimus already have the car specs and colours before they leave Cybertron for the first time to come to earth? Optimus didn't have this when they came to earth in the first Transformers movie.
Plot hole: At the angle of descent and the speed it was traveling (still burning from reentry even), when the space shuttle crashed in the opening of the film, it would not have left much of anything behind. The kinetic explosion that would have resulted would have downed the forest around it for a good distance leaving a crater, and the clean up crews would have been lucky to find any piece of the ship itself still intact bigger than a football. Much less been able to find any discernible remains of the crew. Yet bodies were being taken out in still relatively good condition. And probably most unbelievable is that the glass containers holding the Symbiotes were not even broken.
Plot hole: In all scenes where special or heavy items are used against the sixers, they are 'zeroed' in waves or circles. This can be seen by their stations turning red in clusters. This makes no sense as the stations have fixed positions, meaning that the sixers would have identical positions in the Oasis and have no freedom or own will to move relative to each other.
Plot hole: There was only one T-Rex on the island. When Owen and the others are running down the side of the island escaping the volcanic ash, another dino tries to eat them but then the T-Rex shows up and kills it. This establishes the T-Rex was there in that spot. Owen and the others then wash up back on shore and find the soldiers loading the dinos on a boat and stow away. Then when Blue is bleeding out they have to get a blood transfusion and the only viable candidate is the T-Rex who is now captured and sedated on the ship. How did the soldiers capture, let alone bring the Rex to the ship from where it was seen by Owen back up over hills and rocky terrain? It would have been an all day process just to haul the T-Rex to the ship. It just magically appears on the ship after they stow away on it and can provide the blood Blue needs.
Plot hole: There is no way Anna could know that Hester was going to be at the auction. The circumstances that led to Hester and Tom being captured can't possibly have spread to the Anti-Traction League, they were immediately taken to the slave auction after being captured. Anna also instantly recognizes Hester when she sees her despite the fact that Hester was 8 years old the last time she would have seen her.
Plot hole: Spoiler. Alana discovers the alternate memory pathways in the film while Eve is lying back in the chair with the Mem Scanner on showing it was actually Eve that killed the crew on the pod. But as she's watching it, shots show Eve in the background not wearing the Mem Scanner. So Alana watching the memory feed then would not be possible. It was not recorded and played back until later. (01:19:00)
Plot hole: William is taking a scan of his own brain in the bathroom to try to upload into the robot body, about half way through the film. Later in the film to undermine Jones, he uploads this scan into the robot to give himself a strong ally in the fight who turns the tables. However this Robot William had the brain scan taken that was uploaded into it long before William knew that Paul was turning on him and going to kill his cloned family, which caused the real William to have a near mental break down and fall apart. When the robot William comes in, he's already in on the plan and starts kicking but to get the family back and is about to kill Jones. But there's no way this older brain scan would have reacted this way going into this situation.
Plot hole: The movie establishes the narrative that megalodons have been locked beneath a layer of hydrogen-sulfide and that the first sub to penetrate that layer is their own research sub, thus allowing the megalodon to escape the hydrogen-sulfide layer for the first time in modern history. So, how could there be a megalodon present to at the very beginning of the movie, which interfered with the protagonist's rescue efforts?