Continuity mistake: During the Alejandro/Elena fencing sequence, after he kisses her the first time, her left sleeve is down. The shots before and after have it covered. He slices the fabric off in the next shot. Her right sleeve also came down for no reason. (01:38:15)
Continuity mistake: When Alejandro and Diego fight in the cantina, Alejandro knocks over stalks of corn rolled up in a bundle into the doorway. In the next shot, the corn stalks are standing again. (00:35:30)
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.