How to fix incorrectly labeled/identified media

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So I’m definitely labeling things correctly and putting them in sub-folders correctly, but Plex still is screwing some things up when it scans. For instance, I have a TV show that has some 2-3 min extras (which are in a separate folder than the 1st season and 2nd season). And so for season 1 of this show, Plex is adding the first of each of those extras from each of the extras folders to the first few episodes. So S01E01 has three video files (1 correct that is S01E01, and then two that are the first two extras - one from each of the extras folders). Same with S01E02, S01E03, etc. until there are no more extras and then it just shows the correct episode video file.

How do I fix this? I can’t seem to figure it out. Thanks!

Can you provide some screenshots or literal descriptions of your actual directory structure and filenames? And also a screenshot of what Plex Media Server shows after a scan of the library? For example, my structure for Warehouse 13 looks like:

/TV          <--- My library points here
     /Warehouse 13 (2009)
          /Season 01
               /Warehouse 13 (2009) - S01E01 - Pilot.mkv
               ...
               /Warehouse 13 (2009) - S01E12 - MacPherson.mkv
          ...
          /Season 05
               ...
          /Specials
               /Warehouse 13 (2009) - S00E01.mkv
               ...
               /Warehouse 13 (2009) - S00E22.mkv

So, it has five seasons each with its own directory, and 22 specials. The specials could also have been placed in a directory named Season 00, both are acceptable.

I just tried changing the directory structure but still running into the issue, but I’ll list the new directory structure here:

/TV
      /(TV SHOW NAME)
            /Episodes
                  /Season 1
                        20 episodes
                  /Season 2
                        20 episodes
            /Shorts and Specials
                  15 video files
                  /Specials Sub-Dir #1
                        6 media files
                  /Specials Sub-Dir #2
                        5 media files

Your folder structure is still a bit off; you should not have either of the Episodes or Shorts and Specials directories. And all of your specials should be either in a directory named Season 00 or Specials, with no sub-directories. The documentation provides a very good example at the bottom of the page:
https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/

And, after correcting your naming and directory structure, you may have to perform the steps described here (Plex Dance):

OK, so I think I now have Season 1 and Season 2 correctly showing 1 video file per episode in Plex (by the way, what is the orange indicator in the upper right corner of the thumbnail mean?).

I also have one episode showing for a random Season 6 (which is just one random video file from the “Specials” sub-folder). Is there a way to manually add video files to Plex when it doesn’t detect them (since I’m assuming it might not have the specials video files in it’s database), and fix those that are incorrectly added (such as this one random video file)? If not, I can live with it the way it is, but just wondering.

Thanks!

The orange indicator in the upper-right means that the video/episode is unplayed.

I’m not aware of a way to manually add files to a TV or Movie type library. If the file is named appropriately and is represented in TheTVDB (or The Movie Database), it should be automatically scanned. If it is named correctly and the special isn’t in either of the databases from which Plex is pulling its metadata, you could add it to one or both of them. Or, you may be able to handle it with embedded metadata tags in the file itself (if using M4V or MP4 containers), but that is a little outside of my skillset.

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