Continuity mistake: When Count Olaf grabs Klaus' face, he holds his head with both hands. When it cuts, he's suddenly let go of Klaus' head with his right hand. (00:10:25)
Continuity mistake: When Count Olaf is welcoming the Baudelaires he reach out his hand for Violet and says "Enchante", and you can see his fingers are separated. When it cuts his fingers are clenched. (00:10:10)
Continuity mistake: Right after Olaf has asked who should play the most handsome count it cuts and we see the acting troupe from behind. We can see Luis Guzmán's character holding his glass still by his chest. When it cuts he is suddenly drinking from the glass. Also the people on the couch change positions between the shots. (00:15:50)
Continuity mistake: When Uncle Monty is telling about the Incredible Deadly Viper and he says "My assistant Gustav and I may be the only people who ever seen it", as he stops by the cage he has his hands up. When it cuts his arms are hanging down. (00:31:00)
Continuity mistake: When Violet is done setting the table she sits beside the table and starts brushing her skirt with her hands. When the shot changes she suddenly has her hands together. (00:17:25)
Continuity mistake: When Violet and Klaus are about to close the door in front of Stephano he rams a knife in to the door, and he even twist the knife a bit. This should at least make a mark. Later when Stephano asks if the kids can help him with his bags Violet turns around facing Uncle Monty. Now we can see the door and there is no mark where Stephano rammed the knife in to. (00:36:10 - 00:37:30)
Continuity mistake: After Violet has managed to hit the track shifter with the elf tied on the rope, they begin pulling the rope. It cuts to a shot where we can see the entire rope attached to the shifter with a knot tied in the middle of the rope. When the camera zooms in on the train, in the shot before Count Olaf begin to laugh, the rope is visible and stretched out but the knot is gone. (00:26:25)
Continuity mistake: When the Baudelaires realise they are stuck in the car Violet jumps over the seat in to the front seat. Two shots later, outside in front of the car, we can see her coming over the seat again. (00:24:05)
Continuity mistake: In the beginning, when the camera zooms out of the picture of the burned house, we can see Lemony holding the picture with both hands. When it cuts he's holding it with one hand. (00:16:15)
Continuity mistake: When the train is passing by the car Violet and Klaus are looking at it and smiling. When it cuts to Sunny clapping Violet and Klaus are suddenly facing each other. (00:26:55)
Continuity mistake: When Klaus moves the planks from the window in Olaf's house he gets white spots of dirt on his shirt. When it cuts to him saying, "How could they do this to us" the spots are gone. (00:20:05)
Continuity mistake: In the scene where Violet, Klaus, Sunny and Aunt Josephine are being attacked in the boat by the Lachrymose leeches, you can see Violet has her hair down. When Count Olaf pulls up to them in his boat, Violet has her hair tied back with her ribbon. (01:08:05)
Continuity mistake: While the Baudelaire orphans are trapped in the car, Violet makes the elf head spring forward to catch the track switcher. When she makes her successful attempt, the rope wraps around the handle only once, and the rope does not have the momentum to swing around again. But in the shot as the handle is getting pulled, the rope is wrapped around twice, and moved over a little bit. (00:26:20)
Continuity mistake: When Aunt Josephine hands over the photo album to Violet, it is open to a page with a colored picture. As Violet grabs the album, that picture is gone - it's suddenly open on a different page. (00:48:45)
Continuity mistake: After the Baudelaire's almost were killed by the train while stuck in Count Olaf's car, Mr. Poe moves them over to his car to take them away. Then Count Olaf wants to talk to them and leans against the open car window with his right arm only. When it cuts he has suddenly both arms placed on the car. (00:27:50)
Continuity mistake: Watch the window switches in Count Olaf's 1960 Imperial when the orphans are on the train tracks. When Violet is speaking to Mr Poe on the car phone, the driver's side door appears to have 6 switches in a row (not completely discernible). This means the vent windows on the front doors are power operated (adding 2 switches to the usual 4, with no power lock switch). However the front passenger's side door vent has a manual latch (not used with power vents) which Violet breaks to open the window, and only one switch instead of the two needed for the main glass and vent. And as the train is passing by them, there is a shot of Klaus and Violet in the front seat, and then a lower shot of Sunny clapping her hands. Between these two shots the one switch on the passenger door becomes a set of 2. Several Imperials must have been used for filming.
Continuity mistake: When Olaf says that the children aren't to enter the tower we see Sunny holding her hand down. When it cuts she has her hand up by Violet's chest. (00:13:25)
Continuity mistake: When the Baudelaires walk in to their burnt house while Lemony is narrating and says "But we all discovered that the blaze was started from a great distance", Klaus walks right behind Violet and Sunny. When it cuts Klaus has moved to the side of them. (00:04:55)
Continuity mistake: When Violet and Klaus throw the anchor onto the three cylinders they use to move it, the red and white piece of wood is in the back, but when it shows Violet grabbing the last cylinder to place in the front, the decoracted cylinder that was in the middle is now in the back.
Continuity mistake: When Violet starts to read the letter from their parents, the camera cuts to a shot of the letter. The first paragraph ends with "look hard enough" and the second starts with "We hope to." When Violet reaches that point in the letter, another sentence is added in between the two.
Chosen answer: On the beach, where Mr. Poe comes to inform them of the fire as the movie starts.