After they escape the volcano and Peter finds Amy in the field, Amy picks a flower with two blossoms and hands it to Peter, but when Peter takes it, it only has one blossom. A few moments later in the balloon, it has two again. It is possible that the viewing angle makes it appear as only one blossom. Even in the balloon, when he turns his hand, the blossoms again appear to be only one.
When driving away from the airport, the UNIMOG loses and gains its top several times.
The Glock handgun Karen hands Peter before they enter the city for the second time changes into a Luger when the group enters the mines.
Monroe Kelly's facial scratches lengthen.
Dr Peter Elliot's bruise to his forehead disappears.
Zinj was supposed to have been founded by King Solomon, a great king of the Israelites, yet the only inscription on the stone walls once the party reaches it are Egyptian hieroglyphics.
There should be a lag before a reply when communicating via a satellite.
When they find the white diamonds, they are smooth. Naturally they are very sharp and raw.
Flares fired from flying airplanes would be immediately swept far behind.
Laser beams are not visible when passing through air. There must be dust, smoke, steam or something like that to reflect the light.
When Amy is off on her own with the other gorillas, she does not have the translating glove, but later, when she comes to Peter's rescue, she is wearing it. However, there is a scene prior to Amy's arrival when she goes back to camp and retrieves her translating glove from the tent. The assumption is that she learned how to put it on by herself.
When a bundle of dollar bills is thrown, it appears as if the bills are just white pieces of paper. But American money has a white edge to it, and if you look closely, you can see the corner of the print underneath the flipped corner of the top bill.
An ape removes one eye from Jeffrey, yet later some claim both corpses have eyes. But when Jeffrey is found, his head is turned sideways, so we can not see the right side of his face or his right eye.
Diamonds are often cubic in crystal structure. The diamonds seen in the Zinj mine are hexagonal in crystal structure, making it appear as if they are some other form of crystal. As pointed out in the trivia section, the stones were double-terminated quartz crystals, on loan from the Herkimer Diamond Mines.
The boulders that fall into the water in one scene float.
A large boulder can be seen bouncing off a man.
One explorer takes a photo of a Silverback gorilla, yet the shutter is closed.
Kahega (Adewale Akinnuoye-Agbaje) carries an M14 assault rifle all film but the gun never actually fires once,especially noted in the scene where the camp is under attack he moves the gun like its firing but there is never any muzzle flash.
In an area of ground supposedly cracked by rising wisps of volcanic smoke (this is where Herkermer declares the city of Zinj is true and then kisses a big diamond), a small stream would not flow along the surface but sink down into those cracks.
During the river rafting scene, the actors are intentionally shown not wearing life preservers. Rather, the life preservers are hidden under their shirts giving the actors a bulky appearance.
When the team startles a flock of birds in the ruins you can see the hand of the crew member who launched them, on the right side of the screen[letterbox version only].
On the 1:11:20 mark of the movie, as Monroe walks towards a clearing. You can see 2 crew members behind a bush, on the left side of the screen.
The corporate headquarters is supposed to be in Houston, but the camera shot shows mountains in the background. There are no mountains anywhere near Houston.
When Monroe explains the noises of a Colobus monkey mating season to Karen and Peter, the full moon is shown as seen in the northern hemisphere - but the Congo lies on the equator, from where a full moon would appear to be tipped onto its side.
If a primatologist had a talking gorilla, a logical course of action would be to allow other experts to study the ape for a period of time; not immediately release the ape back to the wild.
The airplane could have flown much higher than the missiles would have been able to reach.
Just as the group enters the cave, Ernie Hudson calls two different characters "Kahega".