Audio problem: At the very beginning where the two young boys cut the eye holes, the sound of cloth ripping is not synchronized with the knife cutting it.
Audio problem: During the scene when Anthony Hopkins is in a dark corner and starts talking to Don Rafael, his lips move at different times than his speech heard on the screen. (01:47:25)
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.