Near to the beginning,not only does a woman in high heels decide to walk into the jungle, they go into a TENT, yet there are shelves visible on the wall, holding things up. Just after this, she decides to walk knee deep into a pond, still wearing high heels.
The helicopter the principals are supposed to be in is the size of a Blackhawk but interior shots of the chopper look more like a 4-seat Robinson.
Near the beginning when Agent Hutchinson is introduced, the camera keeps changing angles from a behind shot to a front shot. Each time this happens, her bands on her forehead keep changing.
Crocodiles lay eggs in mounds on land to get the warmth needed for incubation. Eggs in shallow water would die of hypothermia.
Neither crocodiles nor their embryos produce heat. The eggs (especially those in water) would not show up in heat sensing devices.
Although it is a common mistake, most sharks (including the megalodons) give live births. Therefore the debate of if the eggs were from the crocodile or from the shark there should not have even been a question because megalodons can't lay eggs.
Spoiler: McCormick claims that because the megalodon has swallowed a nuclear sub, it has become a nuclear bomb. Nuclear reactors don't use the right fuel to trigger an atomic explosion.
Neither species in the movie can achieve anything remotely like the size depicted. Current evidence suggests that megalodons topped out at between forty-five and sixty feet. The largest crocodillian on record (Sarcosuchus imperator) has only been found to be in the vicinity of forty feet long.
In the scene where the Megalodon attacks the USS Gibson, McCormick is mourning over the death of his girlfriend. When he puts her head down on the ground to leave the ship, her left arm moves.
When the megaladon leaps over the battleship, not only does the ship not move when the shark lands, there isn't even a wave.
The helicopter the principals are supposed to be in is the size of a Blackhawk but interior shots of the chopper look more like a 4-seat Robinson.
It's unclear why the ship's captain ends up manning a gun.
When the crocodile snaps him up, it becomes agitated and spits him out, then dies. But it's unclear why.
Throughout the movie Jaleel White's character (billed as "Dr. McCormick") is referred to as "Lieutenant," yet he clearly wears the two-bar rank of Captain.