Sadly Plex currently defaults to show items in case a movie is in multiple collections with conflicting settings (same e.g. if you have a collection like the Marvel Cinematic Universe which contains individual movies such as Doctor Strange or The Incredible Hulk but also movies organized by collections such as Iron Man 1-3, Captain America 1-3, Thor 1-3…).
There’s a feature request to change this behavior (however so far it appears only a small number of users is dealing with multi collection assignments with conflicting assignments and having much of an issue with the current approach):
