Continuity mistake: When Violet opens the closet and finds the rat inside you can see a cup beside the rat to the left. When it cuts from a view inside the closet you can see it is a different cup and its handle has changed position. (00:14:20)
Continuity mistake: When the Baudelaires walks out of the burned house Mr. Poe is waiting for them and you can see some fire hoses behind his car. The position of the hoses changes in the distance shot. (00:06:00)
Continuity mistake: As Count Olaf with his acting troupe enters the house and one of them says "Ugly little people," there's a red can and a yellow box beside Violet and Klaus. Two shots later, the two items have suddenly moved closer to them. (00:14:45)
Continuity mistake: When the snake with the message "Impostor" written on it twirls around Uncle Monty's wrist, it's perfectly aligned on his wrist - its tail is by Monty's wrist and the head is pointing up his arm. When it cuts, the head is now by the wrist and the tail is pointing up the arm. (00:39:05)
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 Baudelaires and Aunt Josephine are on their way from Curdled Cave, Klaus holds up the paper drawing of the Eye. He then folds it when Josephine says they all were investigating the fires. When it cuts, he folds the paper again. (01:06:05)
Continuity mistake: When the Baudelaire's come out of their burned house and Mr. Poe is awaiting, as Lemony Snicket says, "I tried to warn you", you can see two police men walk behind Poe's car. When it cuts to a wide shot the police men have walked several metres to the left in quite too short a time. (00:06:10)
Continuity mistake: When the door handle explodes, Violet and Klaus throw themselves to the floor. When lying on the floor their hands change between shots from being close to each other to far away from each other. (01:00:10)
Continuity mistake: When they enter Monty's reptile room the first time there is a lizard and two turtles walking on the floor. When it cuts the creatures have totally changed position. (00:30:05)
Continuity mistake: When we first get to see the anchor hanging there is a sack lying next to the closet. Later when they break the support post making the piece of the house they are standing on wiggle, the sack is gone. And it hasn't wiggled enough to send the sack over the edge. (01:00:55 - 01:02:05)
Continuity mistake: When Poe is about to leave after dropping the kids off at Olaf's, Olaf asks if he wants to stay for a glass of port while gesturing his arm down. When it cuts his arm is up by Poe's chest. (00:12:00)
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: When Sunny picks up the Scrabble letter, you can see the remaining letters are stacked together. Later when the shot change to her smiling, you can see the letters are more scattered. (00:03:45)
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: 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 Aunt Josephine gives the casket to Klaus and tells them to finish the shopping, one of the handles on the casket falls under the roots of the vegetables while the other handle rests on the roots. Two shots later both handles rest on the roots. (00:55:25)
Continuity mistake: When Count Olaf enters with his acting troupe, Klaus and Violet are rubbing the floor and Olaf says "Imagine my surprise." Violet places her left hand on her lap. When it cuts she place her hand on her lap again. (00:14:35)
Continuity mistake: When Count Olaf and the Baudelaires are driving home from court, Olaf says "Children, I've been contemplating our situation." while looking at the kids in the mirror. It cuts as he says "situation" but now he is suddenly looking straight forward at the road. (00:22:10)
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 Violet launch the elf head at the train switching device, the elf head lands at least three feet away from the train tracks. When it cuts the elf head is lying right next to the tracks. (00:26:05)
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.