When Count Olaf asks why the children haven't cooked him roast beef, he is standing on the ground in front of his acting troupe. In the next shot, about a second later, he is shown jumping down from the table (This is due to cutting an extended scene where Olaf gets onto the table and ruins the dinner they have prepared).
When the children are sailing to Curdled Cave, their boat has a rudder. When they are leaving with Aunt Josephine, the boat has no rudder.
At the start of the wedding play, we see Olaf's actresses singing, "Nothing in the world..." and the curtains behind them open. In the next shot, Klaus is sneaking away from the stage, and the curtains are closed (This goof results from the cutting of an earlier sequence).
During the leech attack Violet and Klaus wave their arms in the air, signaling the nearby boat, and Violet's hair is down. When Count Olaf drives up in the boat, Violet's hair is up.
When Aunt Josephine is showing the children her photo album, one shot shows Violet turning the page with the aviation photo directly to the page with the group photo. In the next shots, however, she turns two more pages before coming upon the group picture.
When the Aunt Jo's boat is seen drifting away from the other boat, there is no current pulling her away; so, there is no way that she couldn't have pulled herself closer to the larger boat.
It would be impossible for a train to hit a curve-shaped switch track as fast as it did without a catastrophic derailment.
While Olaf is right in saying that Violet can get married with the permission of her legal guardian, she in turn has to consent to the marriage willingly.
Near the beginning of the movie, some of the Scrabble tiles to do not have their appropriate numerical values stamped into them (G, H, M, P).
Despite being set in the US where the track gauge is standard 4 ft 8-1/2in, the railroad tracks in the film seem to be a wider gauge of over 5 ft.
When Mr. Poe is taking the children from Count Olaf for bad parenting, he carries two suitcases toward the back of his car to put them in the trunk. The Tatra 603 is a rear-engine car; so, he would really have been putting them in the engine compartment.
When 'The Incredibly Deadly Viper' gives the children a fright, we see a shot from the inside of the cage looking out. In this shot, you can see the door to the cage has no handle on the inside. In the next scene, we see the door to the cage being opened from the inside. How can this be if there is no handle on the inside?
During the train scene, the double tracks after the switch are too close together for trains to safely pass each other.
In the scene where Aunt Josephine, Violet and Sunny are in the table, in the shot where Aunt Josephine stands to call for Klaus, you can see for a few frames that baby Sunny (Kara Hoffman, Shelby Hoffman) has a pacifier.
Both Count Olaf's and Mr Poe's cars have open reel tape players built into the car audio systems. In reality, no car audio system has ever included an open reel tape player; the first mass-produced in-car tape player was the 4-track cartridge, followed by the 8-track cartridge, then later the compact cassette.
When the children are locked in Count Olaf's car, Violet frantically pushes all the buttons she can find, hoping they will do something. The tape reel, which plays "The Littlest Elf" theme song, is above her hand. She presses a button and the reel starts to move, but there is no music. In the next scene, the reel is still, then starts to move, and music plays.
The train has a diesel engine's horn, despite the locomotive being powered by steam.
Whenever Sunny bites something, we hear her bite, but don't see her bite it.
At the end, various shots of the Bauedelaire children from previous scenes are shown. The flashback of Sunny at Uncle Monty's home, where she had been following a CGI image of the "Incredible Deadly Viper," shows her to instead be following a little red toy on a string, pulled along by a crew member off camera.
While reading the letter left by Aunt Josephine, Klaus claims to be pointing out how many grammatical errors are in the letter. All of the mistakes he has pointed out (which create a hidden message) are mistakes in Aunt Josephine's spelling, not her grammar. Klaus is meant to be pointing this out to show how smart he is, and if he noticed these errors he surely would not misidentify them as grammatical ones.
Justice Strauss should have been perfectly capable of spotting the loopholes making Count Olaf's plan to marry Violet in the play feasible.
The chore list misspells "separate" as "seperate" in #6, which is also missing a parenthesis at the end of the sentence. Also, since Olaf is giving the list to the children, "pictures of myself" in #2 should simply be "pictures of me", but as written it may suggest his inflated ego.