Make sure you are following Plex guidelines for naming and organization.
See Media Preparation documentation. There are sections for movies and TV shows.
Plex can be picky, especially with TV shows. Best to follow the guidelines.
As you’ve found out, trying to display a TV series as stand alone documentaries will be problematic. You can force the structure by using a “Other Videos” library. However, Plex does not match items in “Other Videos” libraries with the online databases. You’ll have to add metadata manually.
If you do change names/organization, be sure and perform the Plex Dance with the media. This clears out the old, possibly incorrect, data from Plex’s database before re-scanning the renamed files…
Movie example:
/Movies
/Avatar (2009)
Avatar (2009).mkv
/Batman Begins (2005)
Batman Begins (2005).mp4
TV Show example:
/TV Shows
/Grey's Anatomy
/Season 01
Grey's Anatomy - s01e01.avi
Grey's Anatomy - s01e02 - The First Cut is the Deepest.avi
/Season 02
Grey's Anatomy - s02e01.avi
Grey's Anatomy - s02e02.mkv