Are your files named according to the Plex conventions? Link in the sidebar. Please provide a screenshot of your folder structure and file names.

There is no guarantee that anything other than the Plex convention will match all your files. Sometimes it will work, sometimes it won't. The best way is to just go with the recommended conventions, and it will be the most reliable. Filebot is a tool that can do all the renaming and organizing for you, automatically. Tip: You can enter {plex} as the naming format in Filebot.

For the lazy people: Naming Movies | Naming TV Shows | Naming Music

For the even lazier people, this is the proper folder structure and file naming:

Media/
├───Movies/
│   ├───The Dark Knight (2008)/
│   │   └───The Dark Knight (2008).mkv
│   ├───Star Wars Episode VII - The Force Awakens (2015)/
│   │   └───Star Wars Episode VII - The Force Awakens (2015).mp4
│   └───Zootopia (2016)/
│       └───Zootopia (2016).mkv
└───TV Shows/
    ├───Archer (2009)/
    │   ├───Season 01/
    │   │   ├───Archer (2009) - S01E01 - Mole Hunt.mp4
    │   │   └───Archer (2009) - S01E02 - Training Day.mp4
    │   └───Season 02/
    │       ├───Archer (2009) - S02E01 - Swiss Miss.mp4
    │       └───Archer (2009) - S02E02 - A Growing Concern.mp4
    └───Game of Thrones/
        ├───Season 04/
        │   ├───Game of Thrones - S04E05 - First of His Name.mkv
        │   └───Game of Thrones - S04E08 - The Mountain and the Viper.mkv
        └───Season 06/
            ├───Game of Thrones - S06E09 - Battle of the Bastards.mkv
            └───Game of Thrones - S06E10 - The Winds of Winter.mkv