If you replace your content in Plex (e.g. with different versions), the deleted versions will show up in the trash. When you see something in there, it means Plex had the item at one point but no longer has the item anymore. If that is expected (for the reason I mentioned, or some other reason), then just empty the trash. If it's not expected, you will have to correct the issue at the source (Plex) so that the items are still there.