When Matilda sneaks into her parents' room there is a dark-striped jacket hanging on a clothes tree. After she leaves the room and Mr. Wormwood calls Mike into the room, he lifts the clothes tree, but the jacket now turns into yellow and black hounds-tooth material.
It is stated that Miss Trunchbull competed in the Olympics in shot put, javelin, and hammer throw. According to her jersey those were the 1972 Olympics. The hammer throw wasn't added as an Olympic event for women until the year 2000.
When Matilda first arrives at school, she has a sweater on over her dress, and a school journal in her hand. In the next shot, when Miss Trunchbull comes out, the sweater and the journal are gone. Later, when Matilda is inside the classroom, the sweater is still gone, but the journal reappears. Then when she gets home from school, the sweater is back on.
Right before the scene with the newt and the Trunchbull, Lavender is clearly seen filling the pitcher with water before dumping the entire contents of the jar (including the newt) into the pitcher as well. Later on, the Trunchbull pours herself a glass of water, and apparently empties the pitcher, but the glass is smaller than the jar that originally held the newt.
When Matilda arrives at school for the first time, the Trunchbull is coming out the door. The shadows of the kids walking back emphasizes their fear. In the next shot, the Trunchbull's feet and some kids are shown, thus the ground is fully shadowed.
At the beginning of the scene Harry comes home and asks Mike to get a pen and paper to take down his profits for the day. Before they get to the table there is a full shot of the table and no one is sitting at it. A different angle shows Matilda is sitting at the end of the table which was empty a second earlier.
In the scene where the newt jumps on Miss Trunchbull, you can see the math problems are perfectly written on the chalkboard before Miss Trunchbull backs into the board. When she moves forward, two of the problems are smudged and one is mostly erased. In the next shot, all of the problems are intact again.
On Matilda's first day of school when the Trunchbull comes out of the doors, Matilda runs to hide in a gap in the walls where she meets Lavender and Hortensia. After she has finished talking to them and the Trunchbull says "fresh meat", Matilda is standing in her original position in the playground so the Trunchbull brushes her aside. She would not have had time to move to that position.
When Matilda is trying to shut the door with her "powers", she is thinking of all the times others mistreated her. During her flashback you see her mother saying "There's something wrong with that girl," while dying her hair and you can see Matilda is in the background. But when the scene happened earlier in the film, Matilda walks away before her mother says it.
Nearer the end of the film, when Matilda's parents are considering adoption, Zinnia is wearing a gold ring necklace around her neck. Then after she says "Who's gotta pen?" The necklace is gone. Then later when they're all in the car, the necklace is around her neck again.
When Matilda is dancing in the living room using her powers, her socks change. When she is dancing, it appears that she is wearing white ankle socks (visible 1/4 of seconds). A few seconds later after her dance, when she is sitting on the sofa, she is wearing white regular socks.
When Mr. Wormwood takes his kids to the car dealership he states that the junker in the workshop has 120000 miles on the clock. When they begin turning the dial back the first shot (before they actually adjust it) the odometer (incorrectly referred to as a speedometer) reads around 80000 miles
At one point in the film, Miss Trunchbull eats one of the candies without removing the wrapper. However, this is not technically a mistake because some people do eat their candy with the wrapper still on and that trait about Miss Trunchbull only added to her character. (In the original VHS, there is more than one reference to her eating the candy without removing the wrapper.)
While Matilda intimidates the Trunchbull with her magic powers at her house, she gets the Trunchbull's mantle clock to chime 9, 10, and 12, but not 11. However, it is quite likely that Matilda decided to skip 11 and head straight for 12.
At the beginning, when the librarian is telling Matilda about the library cards, Matilda responds, "That would be wonderful." This is still four-year-old Matilda, but the voice-over is obviously Mara Wilson - the six-year-old Matilda actress.
The goof item below may give away important plot points.
Incorrectly regarded as goofs
At the end of the film, Matilda's family moves to Guam to escape the FBI. That wouldn't do much good, since Guam is a U.S. territory and the FBI has jurisdiction there. In some way, though, it might not be considered a mistake, since the movie establishes early on that Harry and Zinnia aren't the brightest bulbs in the box. Maybe they didn't know they'd still get caught. Since Matilda never sees them again, she might think they got away, like the narrator says.