The problem is that The Movie Database and TheTVDB have the show organized differently.
At TMDB, the miniseries is Battlestar Galactica (2003) and the TV show is Battlestar Galactica (2004).
At TheTVDB, the TV show is Battlestar Galactica (2003) and the miniseries are listed as Specials.
Basically, you have to pick which episode ordering to use.
TheMovieDatabase:
/TV
.../Battlestar Galactica (2003) <--- The Miniseries
....../Season 01
........./Battlestar Galactica (2003) - s01e01 - Part 1.mkv
........./Battlestar Galactica (2003) - s01e02 - Part 2.mkv
.../Battlestar Galactica (2004) <--- The TV Show
....../Season 01
........./Battlestar Galactica (2004) - s01e01 - 33.mkv
........./Battlestar Galactica (2004) - s01e02 - Water.mkv
or
TheTVDB:
/TV
.../Battlestar Galactica (2003)
....../Season 00
........./Battlestar Galactica (2003) - s00e01 - Part 1.mkv
........./Battlestar Galactica (2003) - s00e02 - Part 2.mkv
....../Season 01
........./Battlestar Galactica (2004) - s01e01 - 33.mkv
........./Battlestar Galactica (2004) - s01e02 - Water.mkv
You can choose episode ordering at the Library or Show level. Edit the Library/Show, choose Advanced, then pick the desired ordering. You’ll need to refresh metadata if you change episode ordering selection.
If you change naming and organization (rename/reorganize episodes), then Plex Dance the entire show. This will remove bad metadata from the Plex Media server database.
