Plot hole: When Kalgan is torturing Lea, he says that he wants her father's countermeasures in case of emergency. But when she is rescued and finds out MacPhearson is a traitor who is working for Kalgan, Captain Devers is worried because MacPhearson knows all of the ship's countermeasures. If MacPhearson knows the countermeasures, then Kalgon does too, so there is no reason to bring it up while he is torturing Lea.
Plot hole: After Dennis (the first guard assistant) gets killed, the vault is open for several minutes before the old guard arrives. The hobgoblins, however, do not run for their freedom, but patiently wait until the hero, Kevin, comes in a later scene and opens the door. Then they escape as quickly as they can.
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.
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?