When the gang is riding the giant bees, Sean identifies the birds chasing them as "white-throated needletails," which is a species of swift. On the contrary, the birds featured appear to be white-fronted bee-eaters, which are in no way related to or resembling needletails.
When Gabato is piloting the helicopter to the island, his hands are in the incorrect position. The cyclic control (stick) would be controlled by the right hand and the collective would be controlled by the left. Gabato is backwards.
When Alexander is translating from Nemo's journal he says the Nautilus is located at the Poseidon Cliffs. Yet, later in the film Alexander tells Hank and Sean to go a mile and a half in a particular direction towards the Trident Cliffs where the submarine Nautilus is located.
Mysterious Island is supposed to be in the eye of a hurricane. Yet, in the aerial view when Sean and Hank arrive at Trident Cliffs, no hurricane or other clouds are visible, and there is clearly no hurricane around.
The helicopter in Palau has a registration number that begins with N. This indicates it is registered in the United States. Palau as part of Micronesia would have an aircraft registration beginning with V6.
At the very end of the movie as it zooms out from the Earth to the Moon, along the way we see airplanes and satellites, and just before the Moon we apparently pass through some sort of asteroid belt. There is no asteroid belt between the Earth and the Moon.
After Sean falls from the giant bee and injures his ankle against a log several individuals say he has a "dislocated ankle" and his stepfather and grandfather reset it quickly and easily as you would do with a dislocated shoulder. Although it is possible to "dislocate" your ankle it is not only very difficult to do, but due to the unique, and very stable, make-up of the ankle (unlike the shoulder) it only occurs in conjunction with either a fracture or multiple ruptured tendons of the area. Something that is very serious and extremely painful and definitely not something that could be easily remedied by 'popping it back into place' and then the individual being able to walk about and hike.
When Hank and Sean reach the sea, they claim that the sea level has increased by "100 ft in the last 24 hours", yet when they jump in the water they are surrounded by, sea weed, coral and fish. If those rocks were exposed to the air 24 hours before, it shouldn't be covered with coral or other typical sea plants that take months - if not years - to grow.
The Nautilus would have been out of oxygen by the time that Hank and Sean made it to the submarine. Submarines are not made to stay underwater for a long time before they have to return to the surface to exchange the stale air for clean oxygenated air. And, judging by the fact that the Nautilus was submerged for 140 years (or at least that's how old the batteries are, according to the movie), all of the air on board would be extremely stale air and the movie characters would not have survived for very long.
When Hank and Sean work together to break the cryptogram, Hank mentions that one syllable words are dots and two syllable words are dashes leading to a morse code system. The problem with this depiction is that without spaces denoting the end of one character and the beginning of another, morse code is literally indecipherable. For instance "...." (four dots) means "h" but without a space indicator, it could also me "E S" (. ...), "S E" (... .) , "I I" (.. ..) or "H" (....).
Gabato flies his helicopter from the left seat which is normally a copilot or passenger seat while the right seat is the pilot seat. While flying from the left seat is possible, the flight controls in tour helicopters are removed from the passenger station (left seat) and cannot be removed from the pilot station (right seat.
At 18:21 the tail boom and tail rotor break from the Bell 206. Without a tail rotor an American helicopter (with clockwise turning blades when viewed from below) the nose turns right not to the left as animated.
When they land on the (uninhabited) Mysterious Island, the sand over the half-buried Gabby is patted down nicely; but there are large numbers of footprints around him on sand that should be smooth except for the footprints of the other three.