I remember this movie from my childhood, I believe it is from same era as “batteries not included”
The movie has some spaceship on earth with small creatures that live in it, by small I am talking little kid sized. They aren’t evil or mean, but they are fearful of something, either something coming after them, or if I remember right something that lives in the spaceship, I can’t remember exactly.
“Spaced Invaders” (1990) with a young Ariana Richards, perhaps?
http://www.imdb.com/title/tt0100666/?ref_=fn_al_tt_1