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 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)
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)
Continuity mistake: When escaping the lorry with Blue in it, there is an aerial shot where a guard walks past the cab towards the back. Camera swaps to a ground level shot and he is back at the front of the lorry. (01:06:50)
Continuity mistake: When Owen offers Blue some food, he has both arms up in the air. Camera changes and only one arm is raised. (00:31:20)
Audio problem: When Iris is telling Maisie that she will give her a heart attack one day, we see a shot of Maisie over Iris' shoulder. In this shot, Iris isn't speaking but her mouth is moving. (00:21:10)
Continuity mistake: When Iris is looking for Maisie in the fossil room, we see her in a reflection with her arms crossed. When the camera changes to Iris, her arms are by her side. (00:21:00)
Continuity mistake: In the bar, Owen has his hand on the table when Claire mentions about him thinking that he left. Camera changes and his hand is now up by his mouth. (00:17:30)
Other mistake: In Jurassic World, we are told that the Gyrosphere can stop a .50 calibre bullet. When it falls into the sea in this film, Owen shoots some holes in it using a pistol and manages to prise the door off using a small knife.
Continuity mistake: When running from the volcano after escaping the Baryonyx, we see the group level with a group of trees. Camera changes to a front view and the trees have gone. (00:40:40)
Continuity mistake: In the fossil room, Owen, Claire and Maisie turn round a corner when hiding from the indoraptor. Camera changes and Maisie is back turning the corner again. (01:35:00)
Continuity mistake: When they break out the cell, the door is knocked open. Camera changes and the gate is closed with the padlock still attached. (01:18:00)