Continuity mistake: When the letters hits the casket triggering the mechanism, which alarms that mail has arrived, we can see the silver ball begin to roll on the outer edge of the spiral. When it cuts the ball has suddenly went through the whole spiral and reached the hole in the middle in which it falls into. (00:02:40)
Continuity mistake: When Count Olaf spots Sunny and asks who she is, Violet says "Sunny is our sister" and you can see Olaf's hand on Violet's shoulder. When it cuts his hand is gone. (00:10:45)
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 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: As Uncle Monty comes and greets Stephano, Stephano says "Oops, you caught me being a mentor" while bowing down and lowering his arm. When it cuts from behind Stephano he is still standing and lowering his arm again without bowing. (00:36:25)
Continuity mistake: When Olaf arrives with his acting troupe while Violet and Klaus are scrubbing the floor, a small stool can be seen a few feet behind Violet. A couple of shots later the stool has moved right behind her. (00:14:30)
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: When Olaf suddenly stops his car when he is going to buy the Baudelaires some treats, it cuts to the back seat where Violet and Klaus bend forward as if it was a sudden hard stop. However Sunny is sitting completely still as if she isn't moved by the sudden stop at all. (00:22:35)
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 Violet pours the spaghetti out of the spittoon over the strainer, all of it goes out of the spittoon and nothing is left. When it cuts, a spaghetti strand hangs over the spittoon's edge. (00:16:55)
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)
Plot hole: During the play Klaus climbs up the side of the building to save the baby. He gets up and finds out Olaf burned their home with a giant magnifying glass. Later, Klaus uses the magnifying glass to burn the marriage certificate. This is impossible because the device couldn't have possibly been facing or forced to face the stage. The magnifying glass was on the other side of where Klaus climbed up and when he was climbing up he was facing the stage.
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)
Factual error: Before the Leeches attack the boat, Aunt Josephine throws out her banana peel. After she is abandoned by Olaf, the peel finally floats to the surface. A banana peel wouldn't even sink that low especially at the angle Aunt Jo threw it at. (01:10:05)
Deliberate mistake: When Violet and Klaus have the anchor on the three cans they use to roll it on, just before they tip it over the edge, it is obvious the anchor isn't a real anchor. It's too light. When they keep pushing it back and forth, it should tip over because of the weight if it was a real anchor. They shouldn't have been able to handle it like that. (01:01:45)
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.