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)
Deliberate mistake: When Sunny picks up the Scrabble letter, you can hear her biting a piece of it. But when she places it on the board, you can see it hasn't been chewed on. It looks exactly the same as when she picked it up. (00:03:45)
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.
Factual error: Olaf and Violet's marriage certificate bursts into flames after the light from the magnifying glass hits it. The papers would not burst into flames, despite the size of his magnifying glass, it should have just burned a hole. Obviously done to be dramatic. (01:24:25)
Continuity mistake: When Mr. Poe and the Baudelaires first meet Justice Strauss she says that she is Count Olaf's neighbour, it cuts to a view up Olaf's driveway. At the corner of the sidewalk on the left of the screen you can see a tree standing. You can also see that Poe's car is parked right across it. Two shots later when Poe and the Baudelaires walk up Olaf's porch, look between Poe and the Baudelaires. Both the tree and the car are gone. (00:08:10)
Revealing mistake: In the scene where the children are first driven to Count Olaf's house, they turn round to see the house in the distance and while the house is fairly realistic the surrounding scenery and background are obviously matte paintings. (00:08:15)
Continuity mistake: After Aunt Josephine tells how Ike died she starts crying and reaches her arms out at Violet. When it cuts she does the same again. (00:51:15)
Audio problem: When Olaf (as Stephano) jabs the knife into the door when he arrives, it makes a vibrating sound. But Olaf kept his grip on the knife the whole time. It wouldn't vibrate in the door. (00:36:05)
Continuity mistake: When the marriage certificate bursts into flames, the red thing on the certificate in the lower right corner has long threads hanging from it. The length of the threads differ between shots. (01:24:25)
Continuity mistake: In the beginning when the mail is being pushed through the mail box we can see two letters with stamps visible, and the one to the right has a purple stamp. When it cuts three letters with stamps are visible and the one in the middle has a more darkened stamp which is not purple. (00:02:35)
Continuity mistake: After the stove disconnects, right before the phone handle is shown fall off, we can see the handle has already fallen off. (00:59:45)
Continuity mistake: When Violet and Klaus are rubbing the floor, as the door opens, you can see them both lift their heads to look. When it cuts they lift their heads again. (00:14:20)
Continuity mistake: After Uncle Morty, Klaus and Violet agrees that Stephano is an impostor and Stephano returns we see him lifting his arm with the hook on up. When it cuts we can see his arm is suddenly lowered. (00:40:50)
Continuity mistake: Right after Violet and Klaus break the beam which is supporting them during the storm, they begin to run forward in one shot. However, when the angle differs in the next shot, they begin to run forward again. (01:02:00)
Continuity mistake: When the children are on Olaf's boat after Aunt Josephine has been eaten, Mr. Poe and the detective arrive. When Poe says he was wrong about Olaf, Sunny's hood is covering part of her face. When the camera goes to the orphans, you can't see her face at all because she is leaning in to Violet, and when the camera goes back to Olaf, her hood is completely off her face. (01:10:55)
Continuity mistake: When Violet tells Klaus to give her the fire extinguisher, it cuts to him saying "Why?" while holding his hand on Sunny's shoulder. When it cuts back to Violet, you can see in the background that his hand is resting down by her arm. (01:01:10)
Chosen answer: The spy glasses are not explained in the books, but it seems that these are symbols of the fact that they are in VFD, the secret organization we learn about later on in the series. Both Dr. Montgomery and Aunt Josephine's husband and brother-in-law, the Anwhistle brothers, are implied to have been a part of VFD.