After Zorro undresses Elena with his sword, she covers her breasts with his hat. When he snatches his hat away from her, the hand in the close up is not wearing a glove, even though Zorro was wearing gloves throughout the entire sequence.
When Don Diego is fighting Alejandro in the Cantina, there are some hay stacks in the corner. When Alejandro attacks Zorro, one of the hay stacks falls down but in the next scene it's up again in the corner.
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 Don Rafael arrives in the lifeboat, the camera in the boat shows six rowers, all wearing navy blue army uniforms and hats. In the next shot, there are only four rowers, and the two on the left side are wearing white bandannas on their heads.
When Zorro is knocking off guards from their horses in order to get to his horse in the front, during a moment when he's standing upon two horses you can hear him yell and the sound of grunts. Then when you see Zorro attack two guys by slamming them together, the same sound plays.
When Don Raphael and Captain Love are seen in the hacienda's study discussing the plans to destroy "all the evidence" (the mine and its workers), we see plainly Captain Love's sword belt, with no bowie knife scabbard attached. When, shortly thereafter, Zorro fights Love and Raphael because of the missing map to the mine, Love's bowie knife scabbard has reappeared.
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.
When Don Diego and Alejandro are fighting in the Cantina, Don Diego knocks Alejandro's sword out of his hands and on to the ground. In the next shot, he catches the sword as if it was tossed into the air.
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).
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 5 and 6 tons, much more than that type wagon could carry.
At the party, Captain Love is wearing officer's epaulets, but is wearing a senior officer's (double breasted) uniform. The double breasted uniform was used only by those of the rank of major and above.
When the older lady presents the garment to Catherine Zeta Jones she has a younger woman translate to her from Spanish to English. Why would a young woman who grew up in Spain not know how to speak/ understand Spanish while in Mexico?
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.
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.
When we see Alejandro in the guards place were the black Andalusian was taken, he picks up a barrel of gunpowder to stop it from exploding and as he goes out the door leaving a trail of it. When he comes out of the door you can quite clearly see the trail of gunpowder already laid down in front of him before he gets there.
When Zorro first appears, saving the men from execution, he leaps down from a rooftop unto a balcony. Shot from overhead, it's quite obvious he lands on a stunt pad (the stone yields just like a cushion).
The goof items below may give away important plot points.
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 (Zorro) kills Capt. Love, only a little part of the sword crosses the Captain. In the next scene, from above, the sword crosses him to the half, and the point of the sword clearly doesn't match with the rest.