Continuity mistake: In the scene where the Baudelaires and Aunt Josephine are looking in the photo album, Violet turns a page. You can see the photo Aunt Josephine does not want the orphans to see, but when Violet turns to the next page, the same photo is there. (00:49:10)
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)
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 Hurricane Herman has started to destroy Aunt Josephine's house, the stove's gas pipe disconnects, then we see the rotary wall telephone partly fall from the wall. The handset falls completely off, but in a subsequent shot when the stove is ablaze, the handset is hanging sideways from the phone's cradle. (00:59:45)
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 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 Klaus sees that they are sitting on a separated piece of Aunt Josephine's house and he says "Violet, you better tie your hair up", the camera zooms out. If you look closely on the broken edge on the house you can see the edge is firm and smooth. But when it cuts from a view from below as they are looking down you can see the edge on the house is full of broken planks. These broken planks weren't there before. (01:00:30)
Continuity mistake: As Violet and Klaus are looking over the edge of the broken house notice the broken planks. In the next shot the planks have changed. Some are shorter, some are longer. Definitely a different stage of scenery. (01:00:45)
Continuity mistake: As Violet sees the anchor you can see a black broken piece of plank hanging to the right of it. When it cuts the plank is gone. (01:00:55)
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: As Violet approach the closet where the anchor is hanging she has her right hand up by her waist. When it cuts, it's down. (01:01:05)
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)
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 Baudelaires jump over from the broken piece of the house over to the rest of the house, as they land, you can see to the right that there is a big hole in the wall where there should be a window with sprinkles. As they run out of the house, right before it falls in to the lake you can see the sprinkles are suddenly mended. (01:02:05)
Continuity mistake: When the rest of the house breaks off and falls in to the lake, a small piece of wall remains left with the entrance where the Baudelaires are standing. The broken planks left in that piece differ in the close-up shot of the kids and the remaining entrance. (01:02:10)
Continuity mistake: When the children sail away from Curdled Cave with their aunt, the rudder of the boat is missing. The rudder is seen in the shot when they go in and the little baby is at the helm. (01:03:15 - 01:05:40)
Continuity mistake: When the Baudelaires arrives at the Curdled Cave and Aunt Josephine says "You deciphered the clues in my note" she is holding both hands over the edge of the rock on which she is lying. When it cuts only one of her hands are over the edge. (01:04:35)
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: 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: 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)
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.