Hi there
I really didn’t find a solution anywhere, since I’m not quite sure how to google the exact problem, so I thought why not try a forum post. I have trouble with an Anime, it all started when there were 2 different Animes running under the same title (Naruto, Naruto Shippuden). I created a new folder for shippuden and most things seem fixed, except for when I open the first episode of the first season I get S05E01 instead of S01E01.
You probably give Plex a better chance to serve the right stuff by naming your episodes in accordance with Plex’ naming conventions (incl. folder structures)… in particular for TV Shows.
Example (where the Plex library points at the TV Shows folder):
TV Shows
Naruto (2002)
Season 01
Naruto (2002) - s01e01.ext
Naruto (2002) - s01e02 - optional episode title.ext
Naruto (2002) - s01e03 [unrelated stuff in square brackets will be ignored].ext
Naruto (2002) - s01e04.ext
...
Season 02
Naruto (2002) - s02e01.ext
...
Naruto Shippuden (2007)
Season 01
Naruto Shippuden (2007) - s01e01.ext
Naruto Shippuden (2007) - s01e02.ext
....
The episode structures can be a little tricky as the seasons listed in TheTVDb.com don’t match with the DVD releases.