When Pacha is wearing his green cloak his entire under-outfit is brown (which is obviously clear when he raises his arms) but when he takes off the cloak to give to Kuzco, his shirt is white.
The mark Chicha makes on the doorway when Tipo asks to be
measured again disappears soon afterward.
When Yzma and Kronk are visiting Pacha's house, Chicha's headband is blue. When Kronk is leaving the house, it is green.
After Kitty Yzma bounces off the trampoline, the upshot shows the trampoline, but not the guard, the delivery man, or the delivery cart who were in the previous shot.
When Kuzco and Pacha are walking up the cliff, Kuzco asks which foot to use, and they eventually agree to use his right, which would mean Pacha's left. When they eventually step, they both use their right feet.
Jaguars do not travel in large groups. Even if they did, there would not be so many black jaguars in one place, as this color is not as common as that.
Although they are referred to as jaguars by Kuzco, Pacha, and (later) Kronk, the species of cats that Kuzco encounters and runs from are actually black panthers due to their black pattern of fur. Jaguars have a fur pattern that is reminiscent of both cheetahs and leopards.
When Yzma gets stuck being a piñata, 4 children in blindfolds beat her with sticks. For obvious reasons piñata is never played with four blindfolded stick-swinging individuals.
Tipo and Chacha chant the "[Five] Little Monkeys" nursery rhyme starting with 99 when counting down. No bed could ever have room that many monkeys in a small size to jump on it simultaneously.
After Yzma (and Kuzco in a later scene) pulls free from an alligator after triggering the wrong lever, the alligator makes the sound of a dog yelping.
At the restaurant when Kuzco is dressed as a female, he is wearing Pacha's poncho as a dress. He can be seen taking it off and dropping it near the restaurant, so when Pacha is wearing it later, it could well be because he's picked it up.
The room where Kuzco looks at prospective brides has a peacock feather motif. Peacocks are Asian, however the "modernized" pseudo-Incan society depicted here does have commerce with the rest of the world, as shown in the sequel.
The DVD subtitles misspell the "Big" in "Big, dumb, and tone deaf" as "Gig".
When Kronk is pouring the drinks at dinner, there is no bottle on the counter, only the tray of goblets. Also, while he is pouring, look very carefully. He is not pouring into all of the goblets, he is only pouring into the first goblet three times. Furthermore, he is not heard or seen setting the bottle down before popping the cork off of the potion's vial.
The cat that lands on Kronk's head, the baby jaguar, and Yzma (as a cat) all use the same sound effect for meowing.
Pacha uses a cart to carry his goods, but the Inca empire did not use wheels.
The waitress asks Kronk to prepare three pork combos with extra bacon on the side. The Incas were vegetarians and only ate meat on special occasions.
Kuzco is unconscious after the waterfall and Pacha was about to give him mouth to mouth to revive him. However, the movie is based during the Inca Empire which was between 1400-1533. The first ever documented mouth to mouth did not occur until 1732 in Scotland by Dr. Tossach.
Kuzco asks the waitress for an onion log to split with Pacha. Onions were not cultivated by the Incas.
Spinach is served at the dinner with Kronk, Kuzco, and Yzma. The Greeks cultivated spinach, not the Incas.
A split second after Yzma (as a cat) jumps on Kuzco and violently scratches his head, Kuzco can be heard saying "Ow!", but his mouth stays open after he says it.
The theme song describes Kuzco as an icon in "Mesoamerican history". Mesoamerica stretched from Mexico to Central America, not Peru where the story takes place.
In the opening scene in the jungle, there are clearly shown many Venus Flytrap plants. These plants only occur naturally within a 60 mile radius of Wilmington, North Carolina, which is nowhere near Peru.
Kuzco says "What's with the chimp and the bug?" There are no chimps in the New World, and the primate depicted is not a chimp.
The waitress asks Kronk to prepare a chili cheese sampler. Llamas were never milked by the Incas, and dairy products such as butter and cheese were unknown to South America before the arrival of and conquest of the empire by the Spanish.
When Bucky pops the llama balloon, it scares Kuzco, but its loud volume does not wake up the jaguars. A few seconds later, Kuzco says "Ha!" to Bucky, which wakes up the jaguars.
While falling down the stairs after stepping on a cat's tail, Kronk says: "Back, elbow, shoulders", However, he's actually falling in the opposite order: shoulders, elbow, back.
Yzma tells Kronk that the only ones that know she's fired is the three of them (herself, Kuzco and Kronk) forgetting the person who wrote her pink slip which would make it four.
When Tipo tells Pacha that he ate a bug that day, Pacha jokingly says "Oh, has your mother been baking again?" which seems to annoy or offend Chicha. However, Pacha later eats a pill bug at Mudka's Meat Hut and treats it like a delicacy he is familiar with.
The mix-up with the poison occurs because of a peeling label on the bottle, yet it's the only bottle in the entire lab which even has a label so it shouldn't have been that hard to identify.
Yzma, Pacha, and Kronk refer to Kuzco as "Your Highness". This title is reserved for princes. Emperors are called "Your Majesty", not "Your Highness."