At the end of the play we see Violet is telling the people that the play was real in one of the angles we see Justice Stauss holding a book. Then it disappears, and in another angle she's closing the book. Finally, in another angle she has the book open.
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.
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.)
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.)
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 it's at the part where they're on the boat, Klaus shows the drawing of the eye to Aunt Josephine. When the camera turns to her, Klaus folds the paper. Then when it turns it back to him, he has it unfolded in his hands.
When the children enter Count Olaf's house for the first time, and Count Olaf is at the top of the stairs, there is no writing on the palms of his hands. When he walks down the stairs and talks to the children, names and stick figures of the children are on the palms of his hands.
When the children first arrive at Count Olaf's mansion, the metal ring/porthole on the main door swings inwards, downwards. However, when the scene shifts to the interior, the porthole is shown to swing sideways, similar to the door. But when the scene shifts back to the exterior of the house, the porthole door swings back upwards from the inside.
While the children are locked in Olaf's car, Violet shoots the elf head from the window, but the contraption only wraps around the track lever once. Then, after a quick switch to the kids, it's wrapped around twice.
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.
When we meet Count Olaf as Stephano, he mentions that he works in the Monterey Bay Aquarium with sea snakes, and that he has been bitten "347 hundred times", mostly on the face. If this was true, he would be very dead because the poison of the sea snake is 10x more potent than a king cobra's.
When Mr. Poe is taking the children from Count Olaf for bad parenting, he carries 2 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?
The goof items below may give away important plot points.
As Count Olaf is pushing Aunt Josephine's boat away, we cut to Lemony Snicket at his typewriter. On the paper in the typewriter can be seen the words, "...the Viper leapt...", a reference to an earlier scene in Uncle Monty's Reptile Room.
The morning after Uncle Monty was killed, Stephano planned to take the orphans to Peru. However, in that scene, Stephano mentions to the detective that they were going to go to Peru the next day. Then, he says again that they were going to Peru that morning.
When Aunt Josephine's house is falling apart, the stove falls through the floor and down to a dock apparently below the house. However, when the camera pulls back to show the orphans stranded, the dock isn't below the house, but instead located a good distance away nowhere near under it.
In the train scene, when Violet calls Mr. Poe, Mr. Poe is driving alongside the very same train that is about to crush Violet, Klaus and Sunny. However, in the next shot, the train is shown to be coming at them from the right (if you're using the direction from the back of the car to the front of the car as a reference). This would mean that Mr. Poe is: a) driving off-road and b) is merely seconds away from the children. However, when Mr. Poe arrives, he does so by pulling in on the same road as Olaf's car from behind.
Early in the movie, Lemony Snicket says that he and his team only know that the fire was started from afar. At the end of the movie, he knows exactly what happened. However, this film was not based upon just the first book. We are to assume that when the film ends, so does the series itself, so him knowing exactly what happened makes sense because rather than stretching out the series, like Harry Potter, they have wrapped up most of the series in one film, therefore the mystery would be revealed.
Aunt Josephine makes both grammatical errors and spelling errors in her suicide letter. This is intentional, as she is purportedly a stickler for such things and is trying to leave the Baudelaire children a coded phrase.
In Aunt Josephine's supposed suicide note, she purposely included spelling errors as a code for Klaus. She also misuses "it's" instead of "its", which is not one of the clues. However, in the book it is explained that the misuse of "it's" and "its" was to get their attention and prompt them to discover the real meaning.
Count Olaf locks Violet, Klaus and Sunny get in his car to get hit by a train in hopes of killing them. Why couldn't they unlock the doors from the inside by pulling the locks up? The style lock on Count Olaf's car is very hard to pull up from the inside. Plus, he set the alarm when he locked the car. If the children were able to pull the door locks, the alarm would sound and Olaf would be alerted.
Count Olaf brings the Baudelaire orphans for a "ride in the country". But later when Mr. Poe takes them away for bad parenting he is seen taking their bags out of Count Olaf's car. Why would Count Olaf bring their bags with them when he intended to kill them?