While stuck in quicksand, the muck and dirt on Harley's face changes between shots.
During his struggle with Mowgli on the clifftops, Tabaqui's knife appears sheathed in his belt during one frame but disappears in the next frame and doesn't appear for the rest of the scene.
During the scene where Mowgli first enters the room of the stuffed animal heads, William walks in with the elephant knife behind his back. When the scene switches to him sitting down with his hands picking at his pants, the knife is gone, without him setting it down or dropping it.
When the lady points out monkeys, she identifies first one as a macaque, then the next two as Rhesus monkeys (which are also called Rhesus macaques), and the last two as langurs. The ones that she points out as langurs are actually lemurs, which are prosimians, not monkeys, and are not found in India.
In reality, the large rock that Tabaqui picks up would be far too heavy to manually lift.
The barrel on the burning wagon is labeled KEROSENE, but that is the American term; the correct British word is "paraffin".
When Mowgli sees Kitty after his fight with Kaa in the monkey city, right after he jumps towards her, a part of his costume unbuttons then the camera flashes to Kitty. When it flashes back to Mowgli his costume is buttoned.
After Boone sets the temple ledges on fire, people cast distinct shadows on the walls, even though the light source is all around them.
The shot of the guide falling to his death is a clear blue screen effect, judging by the inaccurate proportion of him in comparison to the surroundings.
When the doctor talks to several girls at the river, lemurs are visible. Lemurs live only in Madagascar.
Several of the animals in this film are not from India. The wolves are North American wolves rather than Indian ones, Baloo is a brown bear which do not live in this region, and King Louie is an orangutan (found only on Borneo and Sumatra).
Anacondas are native to South America, not India, where the movie is set.
When Mowgli and Kitty are walking along the river with Mowgli's animal friends, talking about how animals speak to one another using body language, they are carrying a baby White-Faced Capuchin. Capuchins of any variety are not found in India.