Plot hole: There is no way Dirk, Al, and Eva could have made it from the top of the fort to their camels, raced cross the desert and then hid themselves in the sand all before the train were to have met them. The train was barely visible when Dirk saw it through the scope which means it was much farther away to begin with.
Revealing mistake: When Eva goes to check on the man working at the light house and finds his body, the "dead" man's left eye twitches when she checks the other eye.
Revealing mistake: When Dirk and Al are struggling through the desert, chained to the trailer, they slip and fall into the pit. They coast down the slope, thud into a drift and fly through the air and land. However, in the next scene, their tracks are shown behind them as if they had not flown through the air at all.
Deliberate mistake: In the opening credits, there is a newspaper article showing that Dirk Pitt has found the remains of Nungesser and Coli's L'Oiseau Blanc, a plane that disappeared attempting to cross the Atlantic in 1927 before Charles Lindbergh made it. The wreckage in the newspaper photo is totally wrong; it has a radial (round) engine and cowling and a three-bladed propeller. The real plane had an inline engine, square cowling and a two-bladed propeller.
Continuity mistake: In the first boat chase scene a truck comes along the bank of the river with a machine-gunner on the back. When the driver of the vehicle is shot by Rudy with the flare gun, the truck is seen and smoke pours out of the truck's cab to the point where it's hard to see the machine-gunner on the back. Then in the shot where the truck is seen from the boat, there is no smoke at all. Then in the shot of the truck, the smoke is pouring out of the truck's cab again.
Factual error: The scene depicting Muslim praying is wrong. After sujud (bowing down with forehead touching the ground), you are supposed to sit on your legs for tahiyyad. You are not supposed to stand right away, like how the movie depicts.
Continuity mistake: In the boat chase scene with Dirk, Al and Rudi, the glass at the front of the boat gets shot out and then appears intact in the next scene, but is shot into pieces seconds later.
Revealing mistake: When Al is running from the fire in the incineration chamber, fire is shooting out the back. When the fire goes away lights can still be seen in the chamber entrance. The fire should have incinerated them, because this area would be sealed off from the hot area during normal operation.
Factual error: At a stop on the Niger River, before they arrived in Mali, Dirk tells Dr. Rojas of "the angel wing clam" and calls them "Petricola Pholadiformis" and says that "this river is the only place on the earth they are found." Three problems: First, Petricola Pholadiformis are actually called "False angel wing" and are found many places in the world in fresh water (but seldom in the Niger River). Second, what's known as the "Angel wing" shell (no "false" in its name) has "Cyrtopleura Costata" as its scientific name. Cyrtopleura Costata ("Angel wing") is found in salt water. Third, Dirk also said they "glow in the dark"; some varieties of Cyrtopleura Costata shells will glow if exposed to ultraviolet light but none glow from their own internal source. Petricola Pholadiformis shells don't glow at all.
Continuity mistake: When Eva is being choked, at one point the guy is choking her on her bare skin and in another shot, she is being choked over her shirt collar.
Continuity mistake: When Dirk is talking to the rebel leader, while he is loading up the truck, his arms go from being down by his side in one shot to instantly having his hands on his hips in the next.
Continuity mistake: Dirk, Al, and Eva are trapped in the Civil War ironclad. Dirk sends Eva to find fuses for the 150 year old cannon on board the ship. She runs across the room, falls through rotten decking to the deck below and is completely covered with sand. In the next shot as Eva gains her composure from the fall, the sand has disappeared.
Continuity mistake: When the boys are tied in the pickup truck, the truck is moving forward. In the first top down shot of the boys, if you look closely at the ground the truck is moving backwards.
Factual error: Before meeting the Imam, Dirk and Al sat down on a table, discussing. On the background there was the sound of adzan, Islamic call for prayer. However, the adzan was completely wrong.
Factual error: While on the yacht on the Niger River, Dr. Rojas points out Asselar on a map. Asselar is about 230 miles northwest of where she points.
Factual error: While in Labbezanga, Dirk returns to the yacht and says "We're going upriver to Gao." When the buoy later detects something, and Dirk begins to call out the coordinates, "16-degrees 20-minutes North, zero." he gets interrupted by Rudi. The problem is that Gao is at 16-degrees 16-minutes north latitude; if they made it up to 16-20N they would have already passed Gao.