Prior to getting caught by his parents in the kitchen, Max picks up a cookie bitten by Sharkboy with the bite perfectly straight. After getting caught, Max shows his parents the same cookie with the bite in a circular shape.
When Linus captures the three heroes, Max asks "How did you get so powerful?" Linus shows that he has his dream book, which he shows upside-down. In the next shot it is still held at arm's length, but right-side-up.
When Lavagirl's hair is on fire, Sharkboy cools it off by putting water on it. A few shots later, her hair isn't wet at all (it's not in a face shot, so it's hard to see). However, she is supposed to be hot enough to flash-burn anything she touches, so it would make sense that her hair gets dried exceptionally fast.
When Max's parents are going through the tornado to the school to get him, the tornado has enough force so that his dad has to hold on to a tree while the mum gets lifted off the ground. When she's sucked into the tornado, Max's dad lets go of the tree and stands there, not being pulled in at all.
The goof item below may give away important plot points.
Towards the end of the movie when Max is back at school fighting Mr. Electric with his classmates, after he's defeated, there's a wide shot showing all the students in the demolished classroom with Mr. Electricidad, the teacher. It is obviously not George Lopez standing there, but a much younger man with a goatee.