After Pacha saves Llama Kuzco from drowning and lays him on the bank, Kuzco's mouth is wide open and his tongue is clearly sticking out. But when Pacha is about to give the kiss of life, he has to open Kuzco's mouth and the tongue pops out again.
While carrying the unconscious Kuzco in a sack, Kronk presses himself against the castle wall to "hide" himself from the old couple who slowly walk by him. In the next shot, it is clear that the only way the couple could have gone after walking by Kronk is up a huge stairway to the top of the castle, which would have taken considerable time at their pace, yet the couple has completely vanished.
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.
After dragging the unconscious Kuzco out of the water, Pacha puts his ear to Kuzco's chest to check for a heartbeat. As he does, he also puts his right hand over Kuzco, but on the very next shot the hand is no longer there.
Just after Kuzco and Pacha come out of the canal drain, when Pacha says, "It's gotta be one of these," he isn't wearing his hat. After Yzma joins them and attacks Kuzco, Pacha is wearing his hat again.
At the dinner table the position of the plates, silverware, tablecloth and spinach puffs change from shot to shot. The spinach puffs and the small plate Kronk serves one on disappear and reappear in the scene.
When Pacha is sliding on Turtle Kuzcos back away from the guards, he chooses a vile and gives it to Kuzco. When the close up of Kuzco drinking the vile appears, Pacha's feet are not visible on his back.
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.
At the resturant 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 Kronk's New Groove.