Your file naming and structure does not align with Plex requirements. See TV Show Files (Naming & Organizing).
Plex is incredibly picky with TV shows. They must be in a TV Show library. You must follow the recommended file structure and naming.
Rename Wonders.of.Life.2013.S01E01.720p.BluRay.X264-SCENE.mkv to Wonders of Life (2013) - s01e01.mkv.
For The Code, add a Season 01 subfolder and rename like Wonders of Life.
For BBC Horizon, you’ll have to use a Season 2008 subfolder and the appropriate season & episode number in the name. See Horizon - Unknown - Season 2008 - TheTVDB.com
After you rename things, you should perform the Plex Dance for each show (the entire show, not just an episode). It clears bad metadata out of Plex’s database.
