Plot hole: When the group is walking through the jungle for the 2nd time, they have nothing more than their backpacks and a horse to accompany them. Suddenly we see them rowing down a river on a boat and raft. After making peace with the savages, when they have to let a group member go to get medical help, they have been washed ashore as they have been traveling on a single raft since the canoe was damaged by spear attack. How is it that they had a horse and an Indian guide to send away with their injured man? (01:16:55)
Plot hole: Searching for the source of the river, the raft is going downstream. Return trip it's also downstream. Generally, no matter where they are going, the rafts keep floating downstream.
Factual error: The way surveying is done is plain stupid. Percy Fawcett sets up a transit in the middle of a thick jungle, Henry Costin stands 10 feet in front of him holding the rod in one hand and a notepad in the other, then Percy looks through the transit and somehow reads the geographic coordinates out of thin air. This scene repeats couple of times during the movie.
Factual error: An overhead shot of a passenger train supposedly before WWI shows a clip from the 1950s.