I’m referring to the basic OS functionality and file system permissions.
The Plex Media Server is running under a dedicated system account in Linux (default: plex). This system account needs to be able to read your media in order to catalogue and play it. If you want to delete media, the user also needs write permission on your file system.
There’s instructions on a number of use cases in the tips & tricks section.
When you install from the Ubuntu store, you are installing the SNAP package.
SNAP packages run by a completely different set of rules.
The most important rule is: It runs as your username (non-administrative) and is limited to what you can access / delete without using any administrator privileges.
What are you trying to delete ?
Do you have a path name for us?