Continuity mistake: In the police station, after the Klown squirts Mooney with the yellow flowers, Mooney says "So you wanna play games, eh?" If you look at the bottom of the screen, the flowers are still there, but then the the shot cuts to a wide shot, and the Klown's arm and the flowers are gone.
Visible crew/equipment: In the bathroom, when Mike's ex-girlfriend is getting undressed to take a shower a long-necked clown jumps from out of the toilet. Anyone, and I mean anyone, can clearly see the arm of a white guy sticking out of the bottom of the clown's neck controlling the puppet.
Plot hole: When Debbie and Mike are in the pink cocoon room of the circus tent Mike yells, 'Joe Lombardo.' However, Joe Lombardo doesn't die until at least 4 scenes later in the movie, when a Killer Klown edges him off the road and over a cliff.
Other mistake: The Giant Killer Klown at the end of the movie picks up the Ice Cream truck and hurls it into the wall resulting in an explosion that destroys the entire car. The two ice cream drivers say that the way they lived was by hiding in the ice cream truck freezer. First, ice cream truck freezers cannot fit two people and even if they could, the car was blown apart from the back first which would have killed them instantly anyway.