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Continuity mistake: Kronk cuts the rope holding the chandelier with the dagger, leaving a cut piece of rope next to him. The chandelier falls towards Yzma, then she pulls a lever which opens a trapdoor below Kronk, and the cut piece of rope is now a lot shorter than it was when he cut it. (01:03:58)
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Other mistake: Right before Kronk leaves Pacha's house, Chaca's hair has a green stick on the left and a red stick on the right. However, every other time Chaca is on screen, these colours are the other way around. (01:00:29)
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Continuity mistake: When Yzma and Kronk are in Pacha's house, Yzma knocks her cup of tea off the table, then Chicha picks it up and sets it next to the teapot on the table. Three shots later, the cup has vanished from the table. (00:58:15)
Continuity mistake: When Pacha and Kuzco go to Pacha's house to get some supplies, they stop by two men playing checkers. One of the men moves a red piece on the board, but it changes spots a second later. Then, the other man has his fingers on a black piece which wasn't there before; then the piece vanishes a second later. The red piece changes spots again in the next shot, then the man covers it with his hand. In the next shot, the man's hand and the red piece have vanished. (00:57:09)
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Continuity mistake: When Chicha is measuring Tipo's height, she makes a mark above his head on the wood. Two shots later, that mark has vanished. (00:21:11)
Continuity mistake: When Pacha goes to his house for the first time, Chicha is measuring her children's height on the wood. In the following shots, the measurement marks on the wood change a couple of times, then disappear altogether. (00:21:05 - 00:22:17)
Continuity mistake: When Kuzco and Yzma make a dive for the potion bottle, Yzma is turned into a cat simply by landing on the potion bottle. This suggests that a person only needs to touch the potion in order to be affected. However, when Kronk and Yzma are serving Kuzco dinner and are trying to avoid poisoning themselves, Kronk pours his potion drink on himself and is not affected.
Continuity mistake: When Kronk is disposing of the llama body, he runs down a very tall staircase. At the bottom, he runs into two peasants and leans up against the wall. The peasants pass him, walking toward the left side of the screen. Immediately after they disappear from the screen, the "camera" zooms out so you can see the entire palace. Now, the only place the peasants could have gone was up the staircase Kronk had just come down from, unless they wanted to fall off a cliff. If you look on the stairs, though, no one is there. The peasants couldn't have made it all the way up the extremely tall and steep staircase within seconds, so they just mysteriously disappeared.
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Continuity mistake: In the scene where Pacha and Kuzco are drying off after they fall over the waterfall, the slot for the wearer's head in the center of Pacha's poncho is clearly visible when Kuzco takes it and uses it to dry himself off. Following the shot change between when Kuzco throws it and when it lands on the fire Pacha is trying to light, the poncho becomes just a solid green square towel with no hole for the wearer to put his head through, which is easy to see when Pacha hangs it backup on another tree. (00:32:07)
Continuity mistake: When Kuzco smashes Pacha's hill top home, there's no button on the castle, but when he pushes it for the party streamers the button appears in front of the castle. (00:09:35)
Continuity mistake: Right after going over the waterfall, Pacha finds Emperor Kuzko unconscious. When he takes him onto land, his tongue is sticking out. In the next shot, it's back in his mouth.
Continuity mistake: When Yzma is thinking of her first evil plan to kill Emperor Cusko, she knocks the potion off the table in front of her, but after a shot of the plant Yzma is seen again and the table is nowhere in sight.
Factual error: In the movie, there is a whole pack of jaguars. Jaguars are actually solitary animals.
Continuity mistake: In the beginning, all throughout the scenes from Yzma talking to the old peasant, to Pacha coming in and meeting with Kuzco, the tile floor keeps changing colors.
Deliberate mistake: The balloon llama the chipmunk makes has legs which are completely detached. The pairs of legs should be twisted together. Without this, it looks like the balloon has 6 different ends.
Continuity mistake: In the scene where Kuzco falls into the jaguar pit, it shows several scenes with sleeping jaguars with bones scattered around. A few seconds later in the overhead shot, there are no bones in the frame.
Continuity mistake: Before Kuzco throws the crown in the air, there are 6 rays of sun on crown. While it's in the air, there are now 7 rays of sunshine and then back on his head it's 6 rays again. (00:01:30)
Continuity mistake: When Yzma is sitting in the emperors chair she has 4 eyelashes for each eye. When they show close up of Yzma she has 6 for each eye. (00:06:30)
Continuity mistake: While Kuzco is brushing his hair with the llama comb it has 7 legs. When the comb is tossed into the cup it now has 8 legs. (00:01:30)
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Continuity mistake: In the scene where Pacha and Kuzco are hiding in a little room in the restaurant, the door next to them is closed. In the next shot, it's open.