Audio/visual unsynchronized: At the start of the movie, Jimmy ejects Carl from his rocket and Jimmy calls "See you in homeroom!" and Carl replies "OK" but Carl's mouth doesn't move.
Continuity: When Jimmy flies through "John's Oysters" after school, he comes out with a net full of oysters. In all subsequent shots, the net has disappeared.
Factual errors: Jimmy uses a hair from his head to confirm a DNA match to enter his clubhouse. Hair doesn't contain DNA unless it's had skin cells on it.
Continuity: When Jimmy's sneaking out, the picture of the family is hanging on the wall, perfectly straight, halfway up the stairs and with three other pictures surrounding it. The next morning, it has moved to the top of the stairs, is slightly crooked, and the three pictures are gone. The next time it's seen, when Jimmy looks at the picture while walking up the stairs the next day, it's back in its original position and the three pictures are around it again.
Continuity: When we first see the parents under King Goobot's control, Jimmy's parents switch from who is on the left and who is on the right though we don't see them move at all.
Revealing mistakes: When Jimmy is walking down the street holding his stomach, the TV "special report" comes on in the shop window. "Special" is misspelled "Specail."
Factual errors: During the space voyage, the children are living and breathing in the vacuum of space. Jimmy's genius can solve many problems, but he has not invented anything that would enable people to breathe nothing.