The crew ride canoes over a waterfall and get dunked, then emerge on the riverbank completely dry.
Jonah inexplicably disappears from the group after the fight with the conquistadors.
When Hunt picks up the rock to knock out Edwards, he acts as if it is very heavy and can barely lift it, but when he puts it back down he holds in it one hand without dropping it.
When Edwards and the crew are camping for there first night out, the first image is next to the river with a rocky shore with no trees. Then after Hunt breaks the news about the crews moral, Edwards goes outside to get to know the crew. The campsite setting is in a thick forest on the same night.
The boat the crew takes up the river changes and has a second story in some scenes.
Bidwell's ear is still visible on his head throughout the movie after Fontenot bites it off.
When Bidwell is dragged from the campsite by the bear, you can see that the bear is actually pulling a dummy.
When Bart drops the egg as he is returning to the camp, the wire attached to it is visible as it flies through the air.
When Hunt is first leaving to search for the eagle's egg, you can see his boots have modern rubber soles as he climbs up the hill.
When Hidalgo drinks from his mug during the liquor duel with Bartholomew, Hidalgo's mug is revealed to be a prop (no bottom to the mug, and you can see his face through it).
When Leslie Edwards is watching Guy's wife bathing, she has a thong tan line.
When Pratt picks up Bidwell's ear, he sings Brahms' "Lullaby" into it. This song would not be written until 1868.
When Hunt carries the Eagle egg back to camp, a close-up of his feet reveals that he is wearing modern boots with rubber soles and a patterned tread.
Costumes, military uniforms, and head wear are all from the American Revolution period (mid-to-late 18th century), some 20-30 years before the movie's 1804 time frame.
After Hunt and Edwards escape from Hidalgo's gauntlet. Hunt gives Edwards a boost to the top of the rock you can see a microphone in the top left corner of the screen.