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.
Suggested correction: There was a shot showing the T-rex being carried to the boat via helicopter during the beach scene before the transfusion occurs.
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, at least.
Suggested correction: Maybe they did have to sneak around but the director thought making us watch Owen sneaking away at night to take a whiz wasn't really important to the plot.
It was established in the plot's timeline that the ship travelled overnight. A ship like this travels at about 12 knots and would take for them about 9 days to complete that voyage.
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)
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)
Suggested correction: This is incorrect. It shows the door closing twice because it is showing both the third person (camera behind Owen) and the first person (Claire's POV) of the door closing. It was deliberately showing what was happening from different perspectives.
This correction is wrong because it doesn't show different perspectives (which films do at times). In the first shot, the door fully closes before Owen gets to the sphere and before he raises his arms. In the next shot, Owen raises his hands before the door closes and is touching the sphere right as the door closes.
Perhaps your version was out of sync when you watched it. It was definitely just two shots from different angles, if you're watching in UHD on a big enough screen you can even see the camera that catches Owen's reaction.
Audio problem: The sound for the Cessna 208 that our characters take to Isla Nublar is that of a piston engine prop plane, while the plane is actually a turboprop plane. The start-up and cruising sounds are significantly different from what it should be in real life. (00:20:00)
Continuity mistake: When Claire and Franklin shut the hatch on the Baryonyx the debris on top of the hatch changes place instantly. Note there is nothing by the printed "05" in the first shot but there is in the second. (00:39:20)
Continuity mistake: Claire and Eli walk into the room off the hallway side by side. Camera changes and now Eli is about 6ft behind Claire. (00:13:00)
Revealing mistake: When Claire hangs up the phone at the start, the phone is actually off. (00:10:30)
Character mistake: At the beginning they refer to the G8. Russia was removed from the group in 2014, making it the G7. (00:07:20)
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)
Factual error: Owen should be killed instantly by the volcanic ash at the island and he could not run fast enough in order to avoid it. (00:44:15)
Suggested correction: Volcanic ash is is not deadly to the touch and is not high in temperature. At worst it can be toxic if inhaled for long periods of time. There have been plenty of instances where entire towns were engulfed in ash and the residents were fine. What I think this mistake is referring to is something called Pyroclastic flow which is very deadly at 450°C and can travel 80 km an hour. Volcanic ash can sometimes be residue from pyroclastic flow but doesn't have to be precursors or remnants to it. The film never states whether it's volcanic ash or pyroclastic flow but since Owen as well as the dinosaurs inside survive it can easily be inferred to be volcanic ash.
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)
Revealing mistake: When Claire drives the truck and gets it to jump to the boat, the front of it ramps up as it reaches the end of the dock. There was nothing there that could have caused the vehicle to ramp up like that. (00:50:05)
Continuity mistake: When Wheatley grabs the Stegosaurus tooth, his shirt pocket top goes from tucked into his pocket to untucked. (00:49:10)
Audio problem: Claire states that Owen wouldn't let her drive the van for 5 mins. In this over the shoulder shot, her jawline can be seen and it's clear she isn't talking. (00:18:20)
Audio problem: When Zia is on the phone at the start there is an over the shoulder shot of her in the background but her mouth doesn't match what she is saying. (00:09:30)
Continuity mistake: The driving the truck onto the boat scene doesn't make sense. The truck is seen from various angles and in each angle the truck is a different distance from the boat. Some shots it's about 20m max, others it's back to around 100-150m from the boat. (00:51:05)
Continuity mistake: On the beach after escaping the gyro-sphere, Claire's shirt keep changing position. Note the rip on the back. (00:47:30)
Continuity mistake: When the Baryonyx lunges at Franklin, Franklin falls back against a white cabinet of sorts. Camera cuts and he's no longer got the cabinet behind him. (00:38:20)
Continuity mistake: In the bar at the start, Claire's beer keeps changing position without her touching it. (00:17:30)
