Factual error: The Liberty Bell is depicted ringing as the Declaration of Independence is being signed on July 4 (a mistake itself) in the film. The bell actually did not ring on that date, but on July 8, when the Declaration had been returned from the printer and unveiled to the public.
Continuity mistake: After the scene when Aguirre and his men raid the cannibal village they get back on the raft. Aguirre approaches Ursua, lying injured next to his wife, and stares him down. Ursua's wife then stands up to Aguirre and grabs his arm. The shot then changes to a different angle and suddenly the horse appears behind Aguirre so that he can walk into it unexpectedly as he turns around. (00:53:30)