Continuity mistake: Before the play when the man with the arm prostheses takes care of coats he is handed over a coat on his right hook and a hat on his left hook. When it cuts the coat is on his left hook and the hat is gone. (01:12:00)
Continuity mistake: Before the play when Klaus pulls the "Inheritance Law and You" book out of the camel head prop he has his left arm all the way inside the camel head. When it cuts the Camel head is gone from his arm. (01:12:15)
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: In the last scene, when Klaus is in the tower and the light shines through all the mirrors, it is made quite clear he is standing right in the path of the light. Yet, when he walks up to the eye, he no longer is in the light's path. (01:21:20)
Continuity mistake: The marriage certificate that Violet signs and the one that is burning in Count Olaf's hands are not the same. If you look at when Violet signed it she didn't leave a dot over the 'i' in Baudelaire. The one that is burning has that dot. (01:22:35 - 01:24:25)
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: When the crowd is approaching Count Olaf after the marriage certificate is burnt and Olaf says "Not to mention, setting a terrible example to the children", the character played by Cedric the Entertainer is walking among the crowd. When it cuts, Cedric suddenly cuffs Olaf. How did he get on stage that quickly? (01:24:55)
Continuity mistake: When Violet writes the letter B, when she is signing the marriage certificate, the side of the B goes down with a little loop. A few shots later, in a closeup of the signature, the B is different. (01:25:00)
Continuity mistake: At the end, when the Baudelaires walks into their house, we see in a wide shot that they walk up a step on the stairs. When it cuts we see them walk up the same step again. (01:27:00)
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 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.
Continuity mistake: When Violet is signing the 'B' in her last name on the marriage certificate, she connects the 'B' below the line. The shot switches. When it switches back as Violet's signing the 'd', the 'B' is connected above the line.
Continuity mistake: When Count Olaf is driving the kids back from the custody hearing and the shot cuts from Olaf to the kids when Violet says, "Pure evil," Sunny is leaning against Violet, looking as if she is about to fall asleep. When the shot cuts back to Olaf, Sunny is sitting straight up and alert in between her siblings.
Continuity mistake: After Uncle Monty explains why they're going to Peru, he pulls back his jacket and puts his hands in his pockets, revealing the spyglass. In the next shot, his hands are behind his back, not in his pockets.
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.