I don’t think the “Other Mother” in Coraline was a witch, except in very loose terms. In the movie she seemed to be some sort of spider-like monster or alien that could create an illusion that made her look like a human woman. I haven’t read the book so I don’t know if it’s more specific about her origin or true nature.
There are people who would answer that question differently than I would, but my quick answer is that a fairy tale is a short folktale that includes magical elements but (usually) has an ordinary human as the protagonist and (usually) ends happily, or a short literary work written in the style of a folkloric fairy tale.
Fantasy is a broader category that includes any modern (say 1800-present) work of fiction that features significant magical elements. I say “modern” to distinguish fantasy from myths and legends, although fantasy does arguably encompass any story that features magical elements. But I think it’s worth making the distinction between works created by a known author for purposes of art or entertainment and works that grew out of the oral tradition and held religious significance for, or were accepted as histories by, their original audience.
I am not looking to hijack this thread though, so I’d prefer not to get into a debate about this subject. I really just want the OP to specify whether s/he is looking for movies based on fairy tales or would accept any fantasy movie set in modern times. There are plenty of fantasies that aren’t fairy tales, and also plenty of movies based on fairy tales that don’t actually contain magical elements – think of all the romantic comedies that are basically “Cinderella”.