Messy Dr Who Universe

In addition to @Xhaka 's recommendations.

Put a space between Season and the season number, and use two digits for the season number:
Season 02 vs Season2.

If you’re using the new Plex TV Series agent and scanner, you can add the TVDB/TMDB IDs to the folder name. That will help Plex distinguish between the shows. See Naming & Organizing Your TV Show Files.

Example: /Torchwood (2006) {tmdb-79511}/Season 02/Torchwood (2006) - s02e04.mp4

And Plex Dance the shows after any renaming/reorganization.