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.
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.
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.
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.
Stupidity: During the auction, we see the dinosaurs are brought into the room and placed in the middle. Thus blocking half of the bidders from the auctioneer's view. (01:16:40)
Stupidity: This film reveals that the theme park was built upon a dormant volcano. This means that John Hammond either neglected to do a geological survey when picking a location for his park, or simply ignored it and foolishly gambled that the volcano would never erupt.
Suggested correction: Lots of people live right next to dormant volcanos. It can be thousands of years before a dormant volcano erupts. Might be a risk, but not as much as lets say living on a tectonic boundary or in tornado alley.
There's a difference between assuming the risk of living in an area prone to a natural disaster versus building a theme park that's completely reliant on tourism revenue in an area prone to a natural disaster. If a person's home is destroyed by a volcano, they can eventually get a new home, even if it takes a year or two. If a multi-billion dollar theme park is destroyed by a volcano, it's not something that can be replaced so easily, especially since no insurance company in their right mind would cover any of it. Additionally, the island in this film is fictional, which means the writers deliberately chose for a volcanic eruption to be the reason for the evacuation, when they could have just as easily made it so that the military decides to carpet-bomb the island or send in ground troops to gun down all the dinosaurs.
A dormant volcano is a dormant volcano, no reason to think it will erupt only years after you build a theme park on it. The area is not "prone" to a natural disaster. The eruption is a total surprise. Vesuvius erupts once every 2 decades or something and a lot more than a simple theme park is inside its destruction zone (red zone), including 800,000 people. And that is an active volcano. Take a look at Carney Park, a military recreational facility on top of a dormant volcano. Stupid?
Also, the examples you gave are areas with civilian populations that rely on those types of attractions to help stimulate the local economy. Isla Nublar is a privately owned island with no civilian population to speak of, other than park employees, meaning it is 100% reliant on tourism for its revenue.
How many theme parks are built in California, which is severely prone to earthquakes?
That's not an apples to apples comparison. California has a heavy civilian population and theme parks help contribute to their economy. Jurassic World is located on an isolated island with no civilian population and has to rely completely on tourism to stay in business.
Continuity mistake: On Isla Nublar when Claire is running her shirt can be seen without any shoulder sleeves, but for the rest of the film she suddenly has shoulder sleeves.