I think it's an older movie where a small boy becomes small and he befriends some creatures, and there's this spider woman who becomes his friend. He asks someone not to kill them.
It is not "horror" (as per the tag), but this matches the 1996 film version of James and the Giant Peach (based on my favorite Roald Dahl novel). The beginning, where James Henry Trotter is normal sized, is live action, but after he enters the oversized peach, the movie is done with stop-motion animation. He befriends a group of giant invertebrates traveling on a peach, including a female spider.