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 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 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.
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.
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.
While the Baudelaire orphans are trapped in the car, Violet makes the elf head spring forward to catch the track switcher. When she makes her successful attempt, the rope wraps around the handle only once, and the rope does not have the momentum to swing around again. But in the shot as the handle is getting pulled, the rope is wrapped around twice, and moved over a little bit.
When Count Olaf is driving the kids back from the custody hearing and the shot cuts from Olaf to the kids when Violet says, "Pure evil," Sunny is leaning against Violet, looking as if she is about to fall asleep. When the shot cuts back to Olaf, Sunny is sitting straight up and alert in between her siblings.
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.
After the Baudelaire's almost were killed by the train while stuck in Count Olaf's car, Mr. Poe moves them over to his car to take them away. Then Count Olaf wants to talk to them and leans against the open car window with his right arm only. When it cuts he has suddenly both arms placed on the car.
Watch the window switches in Count Olaf's 1960 Imperial when the orphans are on the train tracks. When Violet is speaking to Mr Poe on the car phone, the driver's side door appears to have 6 switches in a row (not completely discernible). This means the vent windows on the front doors are power operated (adding 2 switches to the usual 4, with no power lock switch). However the front passenger's side door vent has a manual latch (not used with power vents) which Violet breaks to open the window, and only one switch instead of the two needed for the main glass and vent. And as the train is passing by them, there is a shot of Klaus and Violet in the front seat, and then a lower shot of Sunny clapping her hands. Between these two shots the one switch on the passenger door becomes a set of 2. Several Imperials must have been used for filming.
When the Baudelaires walk in to their burnt house while Lemony is narrating and says "But we all discovered that the blaze was started from a great distance", Klaus walks right behind Violet and Sunny. When it cuts Klaus has moved to the side of them.
When Violet and Klaus throw the anchor onto the three cylinders they use to move it, the red and white piece of wood is in the back, but when it shows Violet grabbing the last cylinder to place in the front, the decoracted cylinder that was in the middle is now in the back.
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.
In the scene where Count Olaf starts walking from the balcony to the stairs, you can see his right hand when he is saying "lovely home" with no writing. Later when he looks at his hand to remember Violet's name, his hand has writing on it.
When Violet and Klaus make the tent inside their bedroom in Count Olaf's house, they set up the light with the faces of their parents on it in front of it. Except when it shows the shadow of the object outside the tent, the edge of the picture frame isn't showing when it should.
When the Baudelaire children set the table for Count Olaf and his acting troupe you can see and hear them set seven places, but when you are shown the aerial view of the table there are only six place settings.
When Mr. Poe is first taking the orphans to Count Olaf's house, the shot from the front seat shows the children in the back seat and Sunny is wiggling around with her right hand by her face. But when the angle changes she is calmer and is leaning her head on her left hand.
When Violet opens the closet with the rat, she is holding a pile of plates. If you look at the upper plate you can see it has curvy edges. When it cuts from a view inside the closet you can see it is a different plate on top of the pile, because the edges on it are plain.
When Olaf and his acting troupe are gathered and he sits down and says "Now who shall play the most handsome count in the world?", he has his hands folded resting them on his left armrest. When it cuts both hands rests on each armrest.
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.
After the death of Uncle Monty, Stephano says "I do feel somewhat responsible for this tragedy". At the same time you can see a policeman carrying a box passing Violet in the background. When it cuts he passes her again.
When Mr. Poe and the Baudelaires arrive at Uncle Monty's he has his snake twirled around his arm as he reach out to shake Violet's hand. When it cuts the way the snake is twirled around his arm has changed.
When we see Sunny biting on the table we can see her shoulder pads close over the edge on the table. When it cuts to we seeing her hanging on to the table with her teeth her shoulder pads are at least five centimeters below the edge of the table.
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.
When Violet is in the kitchen scrubbing the dishes, if you look right in front of her there is a small rack containing a red box. The end of the red box is over the edge of the rack. When it cuts to Klaus scrubbing, the red box is inside the rack.
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.
In the last scene, when Klaus is in the tower and the light shines through all the mirrors, it is made quite clear he is standing right in the path of the light. Yet, when he walks up to the eye, he no longer is in the light's path.
When the crowd is approaching Count Olaf after the marriage certificate is burnt and Olaf says "Not to mention, setting a terrible example to the children", the character played by Cedric the Entertainer is walking among the crowd. When it cuts, Cedric suddenly cuffs Olaf. How did he get on stage that quickly?
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.
When Count Olaf enters with his acting troupe, Klaus and Violet are rubbing the floor and Olaf says "Imagine my surprise." Violet places her left hand on her lap. When it cuts she place her hand on her lap again.
When Count Olaf and the Baudelaires are driving home from court, Olaf says "Children, I've been contemplating our situation." while looking at the kids in the mirror. It cuts as he says "situation" but now he is suddenly looking straight forward at the road.
When Violet is signing the 'B' in her last name on the marriage certificate, she connects the 'B' below the line. The shot switches. When it switches back as Violet's signing the 'd', the 'B' is connected above the line.
Right after Olaf has asked who should play the most handsome count it cuts and we see the acting troupe from behind. We can see Luis Guzmán's character holding his glass still by his chest. When it cuts he is suddenly drinking from the glass. Also the people on the couch change positions between the shots.
When Uncle Monty is telling about the Incredible Deadly Viper and he says "My assistant Gustav and I may be the only people who ever seen it", as he stops by the cage he has his hands up. When it cuts his arms are hanging down.
When Violet and Klaus are about to close the door in front of Stephano he rams a knife in to the door, and he even twist the knife a bit. This should at least make a mark. Later when Stephano asks if the kids can help him with his bags Violet turns around facing Uncle Monty. Now we can see the door and there is no mark where Stephano rammed the knife in to.
After Violet has managed to hit the track shifter with the elf tied on the rope, they begin pulling the rope. It cuts to a shot where we can see the entire rope attached to the shifter with a knot tied in the middle of the rope. When the camera zooms in on the train, in the shot before Count Olaf begin to laugh, the rope is visible and stretched out but the knot is gone.
After Uncle Monty explains why they're going to Peru, he pulls back his jacket and puts his hands in his pockets, revealing the spyglass. In the next shot, his hands are behind his back, not in his pockets.
When the Baudelaires arrive at Uncle Monty's and Monty says "We have to pack all the equipment" he has a snake whose head is over his shoulder. As Monty close the door it cuts and the snake's head is suddenly hanging down by his waist.
When Count Olaf leaves the car on the train tracks and heads for the shop while locking the car doors with his remote, you can see that the mannequin's stop sign in its hand is pointing to the left. But when it cuts to Olaf hitting the sign it is pointing towards the camera.
When Violet starts to read the letter from their parents, the camera cuts to a shot of the letter. The first paragraph ends with "look hard enough" and the second starts with "We hope to." When Violet reaches that point in the letter, another sentence is added in between the two.
When Mr. Poe and the Baudelaires first meet Justice Strauss she says that she is Count Olaf's neighbour, it cuts to a view up Olaf's driveway. At the corner of the sidewalk on the left of the screen you can see a tree standing. You can also see that Poe's car is parked right across it. Two shots later when Poe and the Baudelaires walk up Olaf's porch, look between Poe and the Baudelaires. Both the tree and the car are gone.
In the beginning when the mail is being pushed through the mail box we can see two letters with stamps visible, and the one to the right has a purple stamp. When it cuts three letters with stamps are visible and the one in the middle has a more darkened stamp which is not purple.
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.
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.
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.
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.
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.
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.
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.
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.
When the train is passing right in front of the car the train signal to the right of the screen is on with a red light. When it cuts the light is suddenly off. It would never have been turned off until the last car of the train had passed.
When Violet and Klaus are setting the table for dinner we can see a chair right next to the edge of the table (on the opposite side of the rehearsing room). But when Violet and Klaus are done setting the table and Violet places the cup of cutlery on the table, the chair has been moved and can't be seen. When it cuts the chair is back.
Right before Sunny bites Count Olaf after the Baudelaires have made dinner there is a shot where Klaus says "No" to Olaf. When it cuts, Olaf's hand has suddenly appeared out of nowhere beside Klaus' head.
Before the play when the man with the arm prostheses takes care of coats he is handed over a coat on his right hook and a hat on his left hook. When it cuts the coat is on his left hook and the hat is gone.
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.
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.
When Mr. Poe is bringing the kids back from Monty, it cuts to a close-up shot inside the car of his hands on each side of the steering wheel. In the next shot his left hand is suddenly on top of the steering wheel.
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.
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.
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.
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.
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.
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.
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.
In Count Olaf's car on the railway, when Violet frantically presses a button, the reel rotates counterclockwise. In the next shot with a close up view, the reel rotates clockwise. In the third shot, just before Violet stops the music, the reel rotates counterclockwise again.
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.
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 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.
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. Remember that Stephano is really Count Olaf in disguise - it wouldn't be out of character at all for him to make this mistake.
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?