The Bounty Hunters leave Earth at the end of the film in a different spaceship to the one they arrive in. In fact, it is the same model used for the ship the Critters arrived (and attempted to leave) in.
In the closing scenes when Harv returns the family to their home, he drives the police car past the barn and stops alongside a fence in front of trees and a field. The same side view of the car is shown a few shots later but now the vehicle is back along side the barn again.
When the rest of the family drags the father in through the front door of the house after he is attacked the second time, a crew member is very clearly visible through a window at the back of the shot.