When D'leh talks to the Egyptian "god", he walks up within arms length of the Egyptian army. In the next shot, he is several paces back.
The film features Smilodon, a genus of sabre-toothed cat that only existed in the Americas.
One of the features of the Nile river is that it flows to the north while the prevailing winds blow towards the south. This made travel along the Nile quite easy. In the film a boat is shown sailing northward on the Nile with its sails up, which would have fought against the wind. In reality, they would not have used a sail but floated with the current.
Several scenes show mammoths galloping. Mammoths were closely related to modern elephants, and couldn't gallop because of their physiology. At best, they could move at a fast trot, like elephants do. They were also never domesticated as pack animals.
While slaves may have been involved in the peripheral tasks involving the construction of the Pyramids at Giza, there is no evidence that they were the primary laborers on the project. In fact graffiti found in and around the pyramids make it clear that skilled craftsmen and paid laborers were the primary builders of the edifices. A town-like location has been uncovered near the pyramids containing a large number of dressed stone houses which housed the laborers, with contents that showed that they earned wages and had possessions that varied from one house to another.
Sabre-tooth tigers had stubby tails, much like a lynx.
In several shots, the stars in the night sky show modern constellations. Due to astronomical movement, the constellations were slightly different 10,000 years ago but not enough to make much of a difference. The distortion of Orion, however, was greatly exaggerated.
The tribes sleep barely clothed in the desert during the night. Temperature differences in the desert vary enormously between day and night because the heat cannot be held in.
(at around 1h 30 mins) In the final scene, the water in the background does not move.
Evolet, a woman who lived 12,000 years ago during an ice age in a primitive tribe has shaved armpits and legs.
Chili peppers and corn are from the Americas. They weren't grown in the "Old World" until after 1500.
The scene with the ships shows the confinement cages made of iron, but the Iron Age did not start until approximately 1200 BC, 8800 yrs after 10,000 BC.
Advanced metalworking is shown throughout the film from jewelry to swords (which were not made from metal until 3,000BC , 7,000 years after the setting of the film) that simply did not exist in 10,000 BC.
The female lead has blue eyes. The genetic mutation for blue eyes occurred 6,000 to 8,000 years ago, outside the film's time frame.
During the terror bird attack, we see men riding horses. The earliest evidence of the domestication of horses dates back to 3,500 BC - some 6,500 years after the time setting of the movie.
The tropical forest is too close to the snowy mountains, with no transition between them.
The terror birds that attacked in the forest lived in South America, not Europe, Asia, or Africa. They also died out at least one million years ago.
The little ice age as depicted in the film is how it would have been in Europe and certainly not in north Africa. Beyond this, northern Africa, including the Sahara across to the Red Sea was just as hot and dry as it is today. The geography in the film makes no sense whatsoever.
The Nile River is shown in the pyramid scene; however it is too narrow to be realistic. The average width of the river is 1.75 miles with the narrowest point (roughly the same distance shown in the film) located in a gorge near where the Aswan dam now stands, hundreds of miles upstream from where the film is set.
Characters refer to the mammoth herd's "lead bull." Like modern elephants, mammoths were headed by a matriarchal female, a lead cow. Bulls never led the herd.