Continuity mistake: As Gromit tries to get to the window with the bomb, he is stopped by being hit hard with a large metal oven paddle which swings in from his front right side. When we see Piella holding it, there is a Gromit-shaped dent in it, but it is dented the wrong way, bulging outward on the side he was hit with instead of indented.
Factual error: In scenes apparently in Japan, all the cars drive on the right side of the road. In actuality, the Japanese drive on the left side of the road.
Visible crew/equipment: When Brother Silence/Cass leaves the house after finishing the campaign at the end of the movie, he opens the front door to leave and there is a glass door/screen there outside the house. For a second you can see a crew member holding the boom mike in the reflection of the glass door. (01:28:10)
Factual error: The Volkswagen Campervan that is used at the beginning of the film has a Zürich number plate, yet the cantonal coat of arms to the right of the number plate is that of the canton of Ticino (red and blue stripe). This is incorrect: The coat of arms should have been a white-blue stripe, which is the coat of arms of Zürich Canton and would correspond correctly to the number plate.
Continuity mistake: At breakfast, the morning after Maria has just arrived at her Uncle's house, the uncle calls Maria's father a coward. He has a glass of brown drink in his hand. He's just taken a drink and the glass is 3/4 full. Maria angrily refutes that her father was a hero and the glass, still in his hand, is now full to the brim. (00:19:20)
Continuity mistake: When Despereaux fights the cat in the rat arena, he hides behind a blue ball of yarn. When the cat hits the yarn, causing Despereaux and the yarn to fly in the air, in the next shot, the ball of yarn vanishes and never reappears again.
Character mistake: The professor identifies the "sea monsters" as plesiosaurs from the Pleistocene. Plesiosaurs became extinct at the end of the age of dinosaurs, nearly 60 million years before the Pleistocene. Of course, the Loch Ness Monster might be an exception.