After Mowgli is stung by bees, his stings completely disappear when walking through the woods in the next shot.
After Mowgli arrives at King Louie's lair, Mowgli has new bloodied wounds on his back and chest, not to mention the bee stings. When Mowgli escapes and runs down the stone steps, not one wound is seen on the front of him. Later, as King Louie looks for him, Mowgli's wounds reappear.
After Mowgli finds the giant snake skin while wandering through the jungle, he spies a cluster of 30 to 40 pieces of fruit in a tree (at 0:27:43 on the DVD), uses a vine to bend the branch down to where he can reach it (now having 10 to 20 pieces of fruit at 0:28:22), breaks the cluster off the tree, breaks one of the fruit off the cluster's stem that is the size of his thumb, and sets the cluster on a tree root beside him (at 0:28:39). While Mowgli is distracted, two small animals grab the cluster with their mouths (at 0:29:12) and run away, each with half of the cluster despite its having a single central stem.
All the elephants in the film appear to be male - they all have tusks, and in Asian elephants, females lack tusks. Males do not form herds as depicted here.
When Mowgli gathers honey and orders Baloo to go to the second mark, the boatswain's chair goes up. Instead, it should have gone down because Baloo is giving Mowgli more rope.
When the primates kidnap Mowgli, some of the gibbons are shown walking on their feet and knuckles on all fours, similar to chimpanzees and gorillas. Gibbons do not actually walk on their knuckles, only their feet.
The credits list a character, drawn as a Nilgai antelope, as "Neelgai deer", which does not exist.
Wolf cubs are born in the spring and grow fast, being almost full-size by their first winter. In this film, Mowgli is away from the pack for a while and Baloo says that winter has come, yet the cubs have not grown at all; however, Baloo clearly lied about the winter, so we don't really know for how long Mowgli had been away. It could have been just a few days.
Gigantopithecuses had been long extinct by the 1890s, when the film takes place. This was a deliberate choice and King Louie is implied to be the last of his kind left.
Despite being a gigantopithecus, King Louie closely resembles a male Bornean orangutan, especially with his face baring two large cheek pads. Of course there is no way to know if gigantopithecus males did not have them also.
The black panther is not a species of its own but in fact a color variation of the leopard. In several scenes it can be seen that Bagheera has spots, which he was described as having in the source novel.
It's been theorized that, due to his size, King Louie could have achieved supremacy over other animals even without knowledge of fire; however, the elephants would still be out of Louie's reach, as they are both large and social.
Several of the animals make the sounds of the wrong species. Many of the monkeys make chimp noises, one of the langurs performs a gibbon whoops.
At mark 1:11:20 when Baloo is being climbed on by monkeys, you can hear Bill Murray's voice get noticeably closer to the microphone in the recording.
Some species not native to India appear, such as a red-eyed tree frog, whilst others are shown in the wrong environment - for example, whilst wolves and jerboas are found in India, they do not live in jungles.
Though Baloo is referred to as a sloth bear, he much more closely resembles a Himalayan bear (a subspecies of brown bear) and, as the name suggests, Himalayan bears live exclusively in the Himalayas.
The wolves in the movie closely resemble Tibetan wolves rather than Indian wolves. Real Indian wolves tend to have a much shorter fur length due to the heat.
Jerboas are native to northern Africa and Asia east to northern China and Manchuria.
For reasons unknown, the monkeys, buzzards, bees, and little fox-like creatures are the only animals that do not speak at all.
Bandar-log ("monkey-people") is incorrectly pronounced in the film. The correct pronunciation of "log" is "logue", to rhyme with "vogue".