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Audio/visual unsynchronised
During Zorro's big duel at the end, he carves an 'M' on Captain Love's cheek. The letter 'M' is made of four lines, therefore four cuts would be required to carve one. If you listen carefully however, you can hear five cuts being made.
When Alejandro is fighting Captain Love at the gold mine, he stops the large wheel from spinning by sticking something in it. The next time we see it, the ladder is in there holding the wheel, but it is not broken anymore. When he jumps off the platform the wheel starts moving and then stops again.
When Alejandro whistles for his horse in the forest, his hat is plain black, without the gold markings seen in the previous scene or when he gets on the horse a moment later.
Alejandro, dressed as Zorro, fights the guards and grabs the "chandelier." The candles were lit, then when he swings on them, they are blown out. In the next shot, they are lit again.
In a blink-and-you'll-miss-it moment at 1:40:20 when Zorro snatches his hat away from Elena (whom he had undressed with his sword), the hand in the close up is not wearing a glove, even though Zorro was wearing gloves throughout the entire sequence.
In the barn, there is clearly a different horse used in the bucking section. Zorro's soon to be horse is large with a thick, wavy mane and tail. The horse that is actually bucking is smaller, with a thin straight tail.
At the mine, the wagon is shown filled with gold. Given the dimensions of the bars since gold is heavy each bar would weigh between 25 and 30 pounds. This would mean that the amount of gold in the wagon would weigh between five and six tons, much more than that type wagon could carry.
When Don Rafael Montero shows a gold bar to the other Dons, he holds it only with two fingers and shows no signs that it's heavy. A gold bar this size would be much too heavy for anyone to hold like that.
Captain Love uses his pistol to light the fuse for the gunpowder kegs. The pure soft lead bullets required for cap and ball pistols are non-sparking, so hitting the fuse would not light it.
When Elena is presented with a sprig of white flower on the beach, and its scent triggers a lost memory in her, she is told the plant grows only in California. The flower used in the film is a Camellia japonica cultivar, a shrub native to (and long-cultivated in) China, Japan and Korea, though introduced to Europe in 18th Century, and thence to America in the 19th. It has no scent at all.
The Mexican flag appearing in the headquarters when Zorro is fighting the soldiers has the red and green areas reversed.
It is mentioned that Elena lived in Spain for the last 20 years. When she's talking with her old nanny and while it may seem to some that she's speaking Spanish, she's actually speaking in a Native American dialect known as Narwack so, yes, she would most likely need a translator regardless of whether or not she's been living around Spaniards her whole life.
It may appear that, when Alejandro tells the soldiers to touch their toes, one of them is in front of the other. But when Alejandro kicks them out the window they are side by side. If you take note when they bend over, you'll notice that one of the soldiers is actually to one side of the other so they are, in essence, side by side and most assuredly not single file.
In the confessional, Elena says she broke the fourth commandment. For Roman Catholics, "honor thy father and mother" is the fourth commandment, not the fifth.
During Zorro's fight with Captain Love at the mine, the captain slips down a rocky slope and for an instant it appears that he loses his sword before it reappears in his hand. In fact, it is his scabbard that is loose, not his sword. You can even see his sword still in his hand.
At the banquet table, Alejandro tells Captain Love that the bandit, Zorro, was certainly 'contrite' for going to Confession. But Love hasn't mentioned the church incident. Unless it's already common gossip, how could Alejandro know? Well, Alejandro knows because it IS already common gossip. This is evident since the others at the table laugh, knowingly, at the jab. If they didn't already know about it there would have been no reason to laugh.
When he dismounts to stop the burning wick, it is obvious Captain Love's saddle cover is made of fake leopard skin material.
When Zorro is surfing down the gulch on a shovel during his fight with Captain Love, a strap holding his foot to the shovel can be seen.
As Zorro is swinging on a tree branch just before kicking Captain Love, the parallel bars used for the tree limbs are clearly visible.
When Zorro undresses Elena with his sword, the clothes are clearly ripped off by a string attached to them, rather than falling off by themselves (See also the item in the trivia section).
When Alejandro accidentally drops the torch in the military barracks, he ignites a trail of gunpowder leading to a collection of barrels. The gunpowder is poured neatly into a trail when he picks up the small barrel; too neatly to have just fallen from the barrel randomly. Additionally when he runs out the door, you can clearly see the trail of gunpowder already laid down in front of him before he gets there.
Don Rafael Montero that says he came via Lisbon and San Francisco. In 1841, San Francisco was still Yerba Buena. The name change didn't occur until January 1847.
Captain Love is identified by his insignia as a cavalry captain. He should be using the model 1840 cavalry saber, but the sword shown has a straight blade more like a modern fencing saber.
When Don Montero outlines his plan to buy California, a key point of his plan is General Santa Anna being in need of money to fund his ongoing war with the United States. The war in question is the American-Mexican War, which would not break out until 1846, five years after the movie is set.
Elena has a nylon zipper on her dress in the last scene, something only possible after WWII.
The movie was set around 1841, but high-pressure gauges that displayed the pressure reading on a dial weren't invented until 1849.
When Don Diego is about to confront Don Rafael for the first time, he begins talking in the shadows but his voice isn't in sync with the picture.
After the big chase scene, as Zorro and his horse canter up the hill, the horse's steps don't match the hoof beats heard.
When the two prison guards return with the bag to carry away the dead prisoner in, an iron door swings back before they pass through. The crew member who pulls it open it is briefly visible at the far right of the screen (widescreen only).
When one of the Dons comes into the room where de la Vega is hiding at the party, stage lighting is briefly visible when the door is opened.
When Don Rafael comes ashore, there are saguaro cactus which only grow in the Sonoran Desert in extreme southeast California.
When Don Raphael meets Captain love, as he leaves there's a flag of Texas hanging on the wall.
There are several mistakes on the large map on Don Rafael's courtyard: the provinces of Aguascalientes and Guanajuato are in the wrong place, the former is misspelled "Aguascal" and the Gulf of Mexico is mistakenly labeled "Bahía de Veracruz". Also, several large mining provinces (relevant for the plot of the story) like San Luis Potosí, are missing.
Tornado, the black horse of Zorro, isn't an Andalusian (as called by Diego) but a Friesian (It has the typical feathers on its hoofs and is of stockier build).
When Alejandro saddles the horse, he does not hook the right stirrup on the saddle horn to keep it out of the way but throws the saddle onto the horse with the stirrup landing on the horse's back and beneath the saddle. Anyone who has ever saddled a horse knows this.