Visible crew/equipment: Two wires can be seen attached to Lavender (because light shines on them) as she floats back to the ground after the Trunchbull charged towards her. This is only visible on video, and has been taken out of the DVD, although you can (barely) see the shadow of the equipment letting her down on the wall behind her.
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.
Deliberate mistake: When the Trunchbull is drinking from the glass with the newt in it, you can easily see that she doesn't actually drink anything, as the water level stays exactly the same. Logical, as the newt is real, but its still very obvious because she drinks for about 15 seconds.
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.