Other mistake: As the brown truck drives away in the scene after the man working in the newspaper office is "harpooned" by a Critter, if you look closely as the truck turns a corner you can see some Critters rolling after it. Well, after they roll past the truck in the bottom left of the screen you can see the Critters roll right smack into another parked car. Obviously the crew forgot to add a turning feature to their Critter balls (which were just some fur taped to a basket ball).
Plot hole: When the old women are painting the eggs, you can see them blowing the yolk out of some. Why didn't they blow the yolk out of the Critter eggs?
Visible crew/equipment: When the Critters are in the restaurant, The Hungry Heffer, as the camera pans across some Critters eating lettuce and other food. If you look closely, you can see one of the puppeteers hands coming out of the bottom of a critter puppet. The puppeteer is wearing a dark shirt with what look like gloves.
Revealing mistake: When a ball of about four Critters is rolling, after coming out of the antique shop, you can see the wires that are pulling it.
Factual error: For most of the movie you can see mountains and large hills in the background. The movie takes place in Kansas and almost all of Kansas is flat.