In interior sequences, Chica's baby son has a plentiful amount of hair. In exterior scenes, the child has less hair, likely indicating that different babies were used.
The coins that The Stranger takes out of one of the two gold bags disappear from his hand when he puts the bags into the water fountain, but reappear when he gives them to Chica.
On most prints (particularly Italian and international versions), no darkness filter is applied to the "day-for-night" sequences, resulting in sequences that are supposed to take place at night/early morning have a clear blue sky. American MGM prints do not contain this error.
Chica is clearly wearing a modern bra under her shirt when Aguilar forcefully throws her onto a bed.
When The Stranger walks through town shortly before encountering Chica for the first time, a cigarette butt with a modern filter can be spotted in the dirt near his boots.
A "dead" Mexican peasant is clearly breathing before The Stranger kicks him over.
When Corvo's dead body lands in front of Aguilar's machine gun, his eyelids tighten.