Continuity mistake: In the part when Lina and Doon are looking at The Book of Ember, they open it to a few pages in. But in a later shot, it shows they are near the middle of the book.
Visible crew/equipment: In the first appearance of the giant mole, the leg of a crewmember/puppeteer is visible at the creature's hind end.
Factual error: In the beginning dialogue when the narrator is talking about the locked box being passed down from mayor to mayor, when it reaches the 7th mayor, the counter is at 47. Later, when Lina is delivering a message to the current mayor, she stops at the portrait of the 7th mayor and says it is her ancestor. In that portrait, the box is visible under his arm with the counter showing 120.
Chosen answer: The light from the sky would have been back-lit by the lights from the city, a bit like how we can't see the stars at night because the sun is too bright. If there were a power failure at noon perhaps the sky could have been seen, however.
Phixius ★