Plot hole: During the play Klaus climbs up the side of the building to save the baby. He gets up and finds out Olaf burned their home with a giant magnifying glass. Later, Klaus uses the magnifying glass to burn the marriage certificate. This is impossible because the device couldn't have possibly been facing or forced to face the stage. The magnifying glass was on the other side of where Klaus climbed up and when he was climbing up he was facing the stage.
Continuity mistake: In the scene where Count Olaf starts walking from the balcony to the stairs, you can see his right hand when he is saying "lovely home" with no writing. Later when he looks at his hand to remember Violet's name, his hand has writing on it. (00:09:20)
Stephano: I've been bitten forty-three...seven hundred times. Mostly on the face. A lot of this has been reconstructed but I think they did a great job even though my moustach is a tad askew.
More trivia for Lemony Snicket's A Series of Unfortunate Events
Question: Where were the children when the house was burning?
Chosen answer: On the beach, where Mr. Poe comes to inform them of the fire as the movie starts.