The F-14s are shown launching small, wing-mounted rockets which are obviously air-to-air missiles (these would be used in shooting down an opposing enemy aircraft), yet the explosions on the ground indicate massive and multiple napalm bomb drops.
When a rocket explodes near one of the characters, they create only a minor explosion. When a rocket explodes anywhere on the island, away from the characters, it is a major napalm explosion that follows upon impact.
Towards the end of the film, when the air raid is launched, two F-14s are shown taking off from the carrier. In a several of the later shots, we see an F-14 and an F-16 flying together.
The aircraft seen in the air-raid are different from the ones that were launched from the carrier.
The Navy F-14's are shown alternately making an attack run with their tail-hooks down, and then without. (Realistically, carrier aircraft would never make bombing runs with their tail hooks down anyway.)
The standard issue rifle of Special Forces is the M 4 A 1 as of 2004, though the M-16 is still being issued to Army reserves and the Marine Corps.
When Professor Phipps and his companions are confronted at the disabled jeep by the giant komodo dragon, he starts shooting with a bolt-action rifle. He fires on semi-automatic (i.e. one shot per trigger pull). Bolt-action rifles are incapable of such fire. Firing one requires the shooter to operate the bolt in order to eject the spent cartridge casing and chamber a fresh round. Special effects were used to simulate semi-automatic fire.
When the robbers arrive at the getaway helicopter after looting the casino, their BMW has California license plates, yet they're supposed to be in Hawaii.
There are no casinos in Hawaii.
The white van driving into Pearl Harbor Naval Base also has California license plates. The BMW SUV with CA plates has a different style of plates on the rear, the front plate is obviously California.
Introductory title says "Isla Damas 312 Miles South of Honolulu". That would be roughly 17N157W. At the end 1:07:30 in the movie the military operation is launched with coordinates 7.35' 240.10', congruent with Indonesia. There is also a real Isla Damas near Chile at 29.14'S 71.31'W. The movie is consistent only with the "312 Miles South of Honolulu" location.
Parts of the island give away position of being in southern California rather than an isolated island in the South Pacific.