When adding a folder, Plex shows the files like this
but when the folder is created, Plex says there are no items in library.
I don’t think this is a naming issue as i have other folders with the same naming convention.
I am running PMS on a headless Ubuntu server, and this is my first added folder after switching, is there some way that I am adding the folder incorrectly?
Server Version#: 1.19.3.2843
It’s very much a naming issue.
But don’t worry, we’ll get you there 
Plex ignores files that don’t follow a certain pattern and are not recognizable as tv show episodes if you want to add them to a tv show library.
The general idea is to have 1 top-level folder that contains your tv shows (you can also have multiple top-level folders assigned to the same library… the underlying rules remain the same).
Here’s an example:
TV Shows <- the folder linked to your Plex tv show library
Show Name
Season XX
Show Name - sXXeYY - optional stuff.ext <- Plex will ignore the optional text such as episode titles after the sXXeYY section
Show Name - sXXeYY.ext
...
Where XX is the season number, YY is the episode number and .ext is the file extension.
Best keep that exact folder structure without adding or dropping anything!
A more specific example (using the built-in standard agents; here: TheTVDb.com):
mnt
harddrive
Plex <- THIS is the folder linked to your Plex TV Show library!
Sword Art Online
Season 03
Sword Art Online - s03e01 - Underworld.mkv
Sword Art Online - s03e02 - The Demon Tree.mkv
Sword Art Online - s03e03 - The End Mountains.mkv
...
Some notes…
- On TheTVDb.com, “Alicization” is simply another season of the main show “Sword Art Online” (season 3)
- Your given file naming / folder structure is quite flawed…
- the top-level folder is named “Sward_Art_Online”
- the episode names use a mix of “SAO” and “Sword Art Online” as their name prefix
- the files don’t have a season/episode pattern in their names
You’ll best re-name that show and verify you’re adding the right top-level folder to that library (e.g. not individual show’s folders). If you stick with the Plex naming schema, you’ll run into significantly less trouble 
https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/
Jokes on me i guess, the files where not readable by Plex, chmod fixed that