In the classroom scene just before Sharkboy and Lavagirl appear, Max throws his dream journal at Linus. In the next shot the dream journal is back on Max's desk.
Sharkboy's back fin falls off of his back as he dangles from the bridge leading up to Ice Princess's castle. In the next shot, it reappears.
The Banana Split boat starts off with two cherries when they launch, and in the next scene, there is only one cherry.
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.
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 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 Sharkboy is carrying Lavagirl towards the volcano, you can easily see it's a dummy he's holding.
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.
When Lavagirl jumped into the water to save Sharkboy, the height of the splash is not proportionate to the height of her leap.
When Marissa heads out to freeze Mr. Electric, a stunt actor filling in for George Lopez can be seen in the back as Mr. Electricidad.
Lavagirl flash burns numerous things when she holds them, yet when she holds the ice she is sucking on it, and it doesn't melt in her hands.
At the beginning of the film Max tells the class that Sharkboy grew gills, but when he is attacked by the electric eels they claim that he'd drown. If he had gills he would have been able to breathe.