Plot hole: Being transported from the west of Costa Rica all the way to Northern California by ship would take about a week. Are we to assume that Owen, Claire and Franklin were staying put in the back of the truck the whole time undetected? They would have to eat and use the restroom, atleast.
Continuity mistake: When Claire and Franklin are in the rolling sphere, the door closes and locks. In the next shot, it closes and locks again. (00:43:10)
Continuity mistake: When Ken Wheatley is pointing his tranquilizer gun at Zia after he shot Owen, he puts the gun in his left hand and uses his right hand to wave his men down, but mid wave, the camera cuts to a different angle and he is waving with his left hand while holding the gun in his right hand. (00:30:00)
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.
Continuity mistake: At the meeting, Benjamin Lockwood is approached by a woman from the side and he says "My bloody medicines." His right hand is forward, gripped around the staff of amber in the close up shot. When it cuts to another angle from the side, his arms are down at his side. (00:15:30)
Other mistake: When Claire and Franklin escape the control room and run down the hill with Owen they stop at a tree with one of the orbs behind it. In the previous film when the rides were shut down, all orbs were back at base except the one Claire's nephews were in, and that one was smashed, so where did this one pop up from, miles from base?
Continuity mistake: When Mills is trying to load the Indominus Rex tooth into his SUV, the sliding side door is open. These doors operate on a catch and lock in place when open or shut until the handle is pulled or the button inside is pressed to automatically close it. As the dinosaurs are escaping, a pterodactyl picks up a soldier and drops it on the vehicle, then in the next shot Mills is panicking and starting to climb under the SUV. In this shot the door is closed. And the soldier being dropped on the hood of the car would not have caused it to close. (01:53:05)