Continuity mistake: The blonde kid starts throwing all the books down until the rack is empty, but a shot later, all the books reappear on it.
Continuity mistake: After Wayne grinds the peanuts, the can on the left with the yellow label changes positions between shots.
Continuity mistake: When Wayne finds the peanuts, the amount of jelly on the knife next to the kid suddenly increases. When Wayne grinds the peanuts, the knife is now laid on the napkin instead of the bread, and it's spotless.
Revealing mistake: After the toy car crashes, the group falls down a hole, but their clothes don't react to gravity, revealing the green screen trick.
Revealing mistake: When the group is riding the toy car, in the wide shots of a real toy car, they disappear.
Continuity mistake: In the scene where Wayne makes his speech at Szalynski Labs, he pretends to stand in a strange shape. When he does so, his speech cards are facing down. In the very next shot, the cards are facing up.
Continuity mistake: When the two couples are riding in the toy car going down the track, the car alternates from (not) having a roof between shots.
Continuity mistake: Near the beginning, just after the people are shrunk, the pattern on the floor keeps changing. In the closeups its really big compared to the people, and from farther away its smaller compared to the people.
Visible crew/equipment: When the Szalinski brothers and their wives are shrunk, they run into a cockroach the size of a sofa. They hide behind some structure with a nut on it. A boom mic is visible in the top-right corner for a second or so.