It’s a known issue.
Plex has designed the feature to prioritize displaying an item over hiding them.
IIRC there’s a feature suggestion asking to reverse this. → Edit: here’s that suggestion: Collection Display Issue
Right now you can bridge some of the gap by using a smart collection for items you want to display in your library (without impacting how other regular collections display them). I’m currently using this for an „Academy Award Winners“ collection (sharing label on the applicable movies; smart collection filtering for those labels)
