Continuity mistake: When the Baudelaires are on the rickety trolley with Justice Strauss, they pass the pebble that Violet drew an X on near the start of the episode. The shape and thickness of the X change each time the pebble is shown.
The Bad Beginning: Part One - S1-E1
Continuity mistake: During Count Olaf and his theatre troupe's performance in the front hall, the bannister and the newel post wobble when Count Olaf grabs it.
The Bad Beginning: Part One - S1-E1
Revealing mistake: Near the end of the episode when the Baudelaires are in bed, the camera goes outside and pans down the front of the house. Once it reaches the next set of windows below the Baudelaires' "bedroom", the camera wobbles slightly.
The Bad Beginning: Part Two - S1-E2
Continuity mistake: When Olaf is standing at that secretary's desk, he reads the calendar and says his name is "haircut." The secretary and the top of her desk are shown several times and in most of the shots, the calendar is visible near the secretary's left arm. However, in at least one of those shots, the calendar vanishes.
The Reptile Room: Part Two - S1-E4
Continuity mistake: Count Olaf enters the bedroom with a knife and says "Oh orphans! [Beat.] Our ship awaits." A few minutes later when we see the same event from another direction, there's no pause, and the delivery is noticeably different, more "oh orphans, our ship awaits." (00:19:45 - 00:23:20)
The Reptile Room: Part Two - S1-E4
Continuity mistake: When "Stefano" puts his ankle up on the table, in the brief closeup his sock is pulled up straight. In the wider shot it's noticeably rumpled. (00:31:05)
The Wide Window: Part One - S1-E5
Continuity mistake: When the Baudelaires are having dinner after Josephine leaves, Sunny is seen placing her rattle into her bowl. In the following shot, she is holding her rattle next to the bowl.
The Wide Window: Part Two - S1-E6
Continuity mistake: The sticker of the smoked mackerel that Lemony Snicket places on the weather chart completely changes position between shots.
The Austere Academy: Part Two - S2-E2
Continuity mistake: In season 1 whenever count Olaf's tattoo is shown, it is always on his inner left ankle (the reptile room part 2, Mr. Poe wipes the makeup to reveal it on the inner ankle, and In the Wide Window part 2 when Sunny chews through the broomstick and Olaf's lag is revealed it is also on the inner ankle. In this episode, after Sunny loosens the laces on Olaf's shoe and the Baudelaires defeat Olaf in the arm wrestling, the tattoo is on the outside left ankle.
The Ersatz Elevator: Part Two - S2-E4
Continuity mistake: Olaf takes out his teeth while she speaks at the auction, then he takes them out again a few seconds later. (00:07:50)
The Carnivorous Carnival: Part Two - S2-E10
Revealing mistake: When the Baudelaires are dressing up again to be the two headed freaks Klaus' glasses are on his face but when the camera switches and comes back again his glasses are gone. (00:07:14)