Revealing mistake: When Nick is being sucked out of the hole/cave, you can see the wires visible from his waist. (01:20:35)
Revealing mistake: In the scene where Amy lets Wayne know that breakfast is ready, she presses a button labeled breakfast. There are other items on the box, such as lunch, dinner, and phone. When they show the board flashing the word breakfast, you can see that the word breakfast is the only word the board can display between flashes.
Audio problem: When Russ jumps from out behind the bush and says, "I say that ant is ours", his mouth doesn't move.
Character mistake: While pitching his shrinking machine to NASA Szalinski claims that reducing the size of a rocket's payload would result in "staggering" savings in the fuel required at takeoff. However, he makes it clear that his machine works by reducing the space between atoms, meaning that the shrunken object weighs the same as the original. Weight is the critical factor in calculating fuel consumption, not size. Anyone at NASA would pick up on that instantly.
Factual error: After their parents give up looking for the kids, there's a "time passing" scene showing the lit attic window from the outside of the house, in which the night grows lighter until it's morning of the next day. But the moon in the picture doesn't move. How can the moon stand still if time is passing?
Other mistake: When Amy hits the button to tell her dad that breakfast is ready, he tries to type "I'll be down in five minutes." However, the message on the strip of paper says "I'll be down in five mimmicks." Amy says, "Typing with his gloves on again." Even if someone was typing with their gloves on, the blatant misspelling would not happen.