Continuity mistake: When Violet is in the kitchen scrubbing the dishes, if you look right in front of her there is a small rack containing a red box. The end of the red box is over the edge of the rack. When it cuts to Klaus scrubbing, the red box is inside the rack. (00:14:15)
Continuity mistake: When the two ladies are done singing before the play the carpet on the stage is open wide. When it cuts to a close-up of Klaus looking around you can see in the background that the carpet is closed. (01:16:30)
Continuity mistake: When Violet and Klaus are setting the table, Violet puts her first plate on the table. When it cuts she puts it on the table again. (00:17:15)
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)
Other mistake: When the children run into Captain Sham (Count Olaf in disguise), Aunt Josephine says that the children will make them a meal of puttanesca. You need the stove to make puttanesca but Aunt Josephine would never let the children anywhere near the stove because she was terrified that it would burst into flames.
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)
Factual error: When Klaus burns the hole through the certificate, Count Olaf looks right through the hole into the magnified sunlight. His eye would be severely damaged if looking into sunlight through such a powerful magnifying object. (01:24:25)
Deliberate mistake: In the shot where the camera zooms in on the car, after they realise they are standing on a train track, it is obvious that the car would be hit by the train even if they managed to change tracks. The car's hood is parked right above the other track. (00:23:45)
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)
Chosen answer: On the beach, where Mr. Poe comes to inform them of the fire as the movie starts.