Continuity mistake: When Matilda makes the chalk write the message on the blackboard, the writing changes. Watch the "Agatha," especially. The handwriting changes and the comma changes length, as well as most of the message changing. Also at the end of the message Matilda "writes" two long lines under it, which cross over. Yet later when Miss Trunchbull flies off the globe you can see there is just one line under the message, not two.
Continuity mistake: When Miss Trunchbull is in her home searching for the person in her home, she jumps down off the second floor to the first without using the stairs, a chandelier falls to the floor and shatters. Moments later when they show that area again, the chandelier is gone from the floor, in fact it's seen back up on the ceiling.
Continuity mistake: When Miss Trunchbull walks out of the school doors, at Matilda's first day of school, she walks down the steps and everyone runs a far distance away and the crowds of children are fairly scattered and distant. Yet in the next shot of the Trunchbull's feet, there's suddenly a large definitive crowd standing much nearer to her. Then as the Trunchbull walks down the stairs, in an overhead shot the crowds of children back far away from her, yet in the following shot the crowd is back to standing right by the stairs.
Continuity mistake: When Matilda is talking to her mum about her first day of school, and her mum is on the phone, Matilda holds her books against her chest, and between shots (both of her arms are against the books) her arms go from, the left arm being above the right, to vice versa then to back.
Continuity mistake: In the showroom, there is an old car covered in dust with "$100" witten in the dust. Harry then adds two more zeros after this. Through the garage scene, the two zeros noticeably change. They go from drawn far apart and unperfectly round to touching each other and perfectly round.