Other mistake: Blondie suffers from severe sun burn wounds in the face, after the capture and dragging through the desert. The wounds look perfectly realistic, but disappear or change several times. The burns are completely gone shortly after leaving the monastery. Such burns would leave scars and traces for at least weeks.
Other mistake: About 20 minutes into the film, Tuco is arrested by the sheriff who rolls out a Wanted poster which has Tuco's picture. However, as can be seen (but only visible for a second or two), the name on the Wanted poster says Guy Calloway, who was a character in Leone's previous film For A Few Dollars More, who had a bounty on him (and a poster) and was killed by Col. Mortimer early in that film. Leone was notorious for trying to reuse props to save money (the Al Mulock story being the most infamous example), and possibly just reused the old poster with Wallach's picture on it, figuring nobody would notice.
Other mistake: Director Sergio Leone uses one of his trademark filming techniques throughout this film, where anything outside the camera frame doesn't exist. Several times the characters react to situations and other characters when they come into frame that they logically would've seen much sooner. For example, at one point Blondie and Tuco are walking and stumble across an army camp. Even though in reality they would have been walking toward it for a long time and would have been aware of it, they react with surprise the moment it appears on screen.