Did you also “Plex dance” the shows involved?
Also structure is very important to Plex for TV shows:
A basic format is:
TV Shows <— The library points here
---------TV Show Name (Year first aired if needed) <— This folder holds the season folders
------------------Season 01 <— This folder holds all the episodes for season 01
-------------------------ShowName - s01e01 - Episode Name.ext
-------------------------ShowName - s01e02 - Episode Name.ext
-------------------------And so on for the rest of season 01
------------------Season 02 <— This folder holds all the episodes for season 02
-------------------------ShowName - s02e01 - Episode Name.ext
-------------------------ShowName - s02e02 - Episode Name.ext
-------------------------And so on for the rest of season 02
------------------Season 03 <— This folder holds all the episodes for season 03
-------------------------ShowName - s03e01 - Episode Name.ext
-------------------------ShowName - s03e02 - Episode Name.ext
-------------------------And so on for the rest of season 03
This repeats for each show and you can have more than one “TV Shows” directory but the library needs to point at each of them.
Note: The year after the show name is only normally needed or desired if there is more that one show with exactly the same name. Check http://thetvdb.com/ if you are not sure and match exactly the name used there.
There are naming methods other than the above that work but this does work 99.9% of the time.
If you are going to use Plex it is best to use the proper naming conventions so Plex makes the best match possible. Trying to force Plex to use other naming methods is just asking for frustration.