This is the story behind the ride as presented by USJ:
https://www.usj.co.jp/e/jurassic-park-t ... -dinosaur/
Since its opening in 2001, Jurassic Park has been a favorite of guests around the world. Within its grounds, there is a hidden area inhabited by wild Pteranodons, for which human management is kept to a minimum.
The Jurassic Park development team researched for years in order to create a dream attraction that would allow guests to fly through the sky with these dinosaurs.
Finally, they trained the wild Pteranodons and managed to get them to fly while stabilized. However, though they have been thoroughly trained, they are still wild dinosaurs.
They say that it's possible to suddenly lose control while in flight, so beware...
Now, to dig a little bit into the movie canon, this roller coaster is indeed based on the flying Pterosaur scene from Jurassic World:
[youtube]http://www.youtube.com/watch?v=LBTE3aH5gpw[/youtube]
However, those privy to the series will also know that the new movie park is titled "Jurassic World", with "Jurassic Park" having closed after the first movie.
So while this roller coaster is based on the events of the latest movie, USJ provides an alternative story "theme" behind the roller coaster that takes place in Jurassic Park, rather than Jurassic World. So yeah, movie logic need not apply.
Oh, and Pterosaurs are still not flying dinosaurs. Flying reptiles my friends, reptiles.