When the kids are in the back of the police car yelling at the police as they approach the house their voices are muffled as if completely enclosed in a car despite the front, driver-side window being open and a metal grate separating the front and back of the police car.
When DJ, Jenny and Chowder are jumping out of the back of the police car for safety, they're not wearing their water guns and they are nowhere to be seen. However, in the next scene, their guns are around their arms and ready for use.
When Jenny goes to sell candy to the Monster House, DJ and Chowder run up and we see the "KEEP AWAY" sign on the left behind Jenny mostly covered by Chowder. Next shot the sign is less than three feet from her and in front of her.
The driver side on the police car switches between the two times it is seen. The first time it is shown as a normal car in the United States. When the police arrive to arrest the kids it pulls up onto the curb with driver side moved to the incorrect side.
When Chowder sprays Jenny with water from his water gun in Nebbercracker's basement, the water mark disappears in the next shot of her which is just after a brief shot of DJ. The water could not have dried that quickly.
Before DJ, Chowder and Jenny went to Nebbercracker's house to try out their dummy plan, the scene focuses on a picture DJ took, which is of the tree outside the house. When the scene changes and becomes real, it showed the three of them walking towards the house, which was on the right side of the screen. If DJ had taken the photo from his house, they should have been moving towards the other side where the house should have been.
The goof items below may give away important plot points.
Jenny says they have one hour, probably implying she has one hour until her Mom picks her up. She arrives at DJ's house early in the morning, and it is dark when her mother arrives, meaning she was there for far more than one hour. We also see her make or receive no calls to/from her mother.
When the dog which is 'eaten' by the house first appears, it squats to pee in the manner of a female dog. At the end of the movie, when it appears again, it hikes its leg up and pees as a male dog. The dog is referenced in the credits as "Kevin". Male dogs are also known to squat in the manner of a female when they pee, so this is quite a possible thing.