Other mistake: Later in the movie, when Alejandro is getting his horse, he lights the cannon. Then he throws the torch down and it lights the powder. He picks up the keg of powder and runs out the door. As he is running, you can see that there is already a line of powder on the ground that he is running over. (00:51:35)
Other mistake: In the ending shots, when the hoist is bringing up the last of the gold to the wagon, why is the wagon covered up if they still have gold to put in it? (01:52:40)
Other mistake: Near the end of the film there is a stand-off, if you look in the sky an aeroplane flies by.
Answer: He recognized that Bernardo was really Diego de la Vega and he realized that the young Zorro he had seen earlier could not have been Don Diego. He then deduced that the new Zorro looked similar to Don Alejandro (and was probably warned by Captain Love that Don Alejandro was hiding someting) and made the decision.