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. (01:20:20 - 01:23:00)
Other mistake: Near the end of the closing credits, when the Warner Bros. Copyright appears, you'll see the very first word "All" spelled incorrectly as "Al" in "All material is protected by Copyright Laws of the United States and other countries throughout the world." (01:26:40)
Continuity mistake: In the scene with Sinbad and Howard in the radio place, Sinbad gets enraged, then throws the package (thought to be a bomb) and Howard hits the deck. The package lands at Howard's head, but in the next shot, it's way over to his left.