During the launch scene at Yellowstone Lake Cpt. Lewis orders "Gass, take the point." Later, when they spot the canoe on its side you hear Sgt. Gass say "That's our point canoe." No explanation is ever given as to how or when the point canoe was changed.
The film depicts a number of troops in the expedition meeting their deaths at the hands of natives or other causes. As a matter of fact only a single member of the Corps of Discovery died in the entire expedition - Sgt. Charles Floyd, of acute appendicitis.
The romance between Clark and Sacajawea, and the Indian warrior's jealousy of Clark are fiction. Sacajawea was married to a French-Canadian fur trapper when she met Clark, and there no historical basis to suggest that her and Clark's relationship was anything other than professional. Needless to say, she did not accompany Clark back to Washington, as shown in the film.
When Clark launches his canoe on Yellowstone Lake he is in the very back, there is cargo in the middle and another paddler up front. For the next three shots of him watching Sacajawea running along side he is still at the back, but in the next wide-angle shot and subsequent shots he is alone in the middle of an empty canoe. Someone apparently realized that Sacajawea wouldn't be able to get into the original canoe, thus the change, and didn't feel it necessary to go back and re-film the launch scene.
Indians create an ambush using a net drawn across the river to stop Lewis and Clark. Upstream the Indians push logs into the water to hit the canoes. The team try to push them away causing the canoes to rock - during which you can see the shiny hull of two canoes come out of the water - clearly made of fiberglass.
During her talk with Sacajawea, Julia calls The President's Mansion "The White House". The scene takes place in 1806; the earliest reference to The President's Mansion being called "The White House" is in 1811.