In the studio shots, there are no windows in the airplane.
The shadows reveal obvious studio shots when the two kids are climbing around on top of the poachers truck, and during the close-ups of the airplane.
For the scene where Xixo brings the soldiers and the doctor to the man in the sand; after he shakes the sand off himself, he sits up. There is a long shot of the man with his shirt unbuttoned and clean. In the next cut, his shirt has sand all over it and is buttoned up.
When Dr. Taylor is shown in the airplane losing her dress (both at the beginning and ending of the film), she is wearing pink panties and a white bra. When she takes off her dress at the water windmill, her bra and panties are both pink.
The small aircraft goes from about 2000 feet in the mountain areas (with wires visible) to 25,000 feet very quickly, a physical impossibility.
When the plane is flying through the rock formations, suspension wires are clearly visible on two occasions.
Just after the rhino attacks the Doc Taylor, the other man pulls himself on top of the branch. A wire is visible, attached to his shirt to stop him from falling.
When Dr. Taylor climbs up the tree to escape the rhino, a horizontal wire that was presumably used to make the tree shake is visible just below Dr. Taylor.
Wires holding up the plane are visible while it's being blown into the tree.
Xixo is thrown from the front of the poachers' truck as they slam on the brakes. When he hits the ground, a mat hidden beneath the sand pops up beneath him, a split second before the truck rolls over him.
The African soldier jumps out of the jeep with nothing in his hands but binoculars. He jumps back into the Jeep to drive away, leaving a large metal box behind.