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: 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.