Continuity mistake: When Pacha and Kuzco fall down the canyon wall only to get stuck in the narrow gap they have to work their way back up to the rope, but when Pacha fell through the bridge just seconds before he had a clear view of the river below. There was no narrow canyon blocking the way.
Continuity mistake: When Kronk offers Kuzco the poison, he runs out of the room because his spinach puffs are burning. He takes the poison with him. When he returns he is carrying only the spinach puffs and the cups appear back on the table.