Server Version#: 1.31.2.6810
Player Version#: Plex Web 4.103.2
TLDR: Check your library folders if you move music files around and make sure to remove folders that are no longer in use or duplicate a file path.
I recently changed some tags in my music files so I could make albums sort and show up in compilations, EPs, Demos etc… Everything was fine I got it to work and then for some reason all the files I changed the releasetype tag on were showing up twice in the album even though there was only one music file. So for example on one of my live DMB albums I had 2 entries for the same song.

Track 3, 5, 7. Were pointing to the same file. I spent days emptying trash, rescanning, optimizing database, refresh metadata, plexdancing, nothing seems to fix this. I was scratching my head for sometime, and then I figured it out. So I am posting here in case someone else has the same situation.
In my main music library I had a bunch of folders, way to many and wanted to consolidate all those folders for better file management. I created the main folder and added that to the plex library with all the other original 20+ folders. I then moved files into the main folder and reorganized them.
Plex kept all my play counts metadata all that was perfect. Except now I got duplicate entries for many of my albums and I had no idea why. I ignored it for a long time cause both would play if you hit play. It was just visually annoying and if you listened to an album it would play a song twice in a row sometimes.
Anyway, I finally got annoyed enough that I dug in deeper. Here is what fixed my issue. The old folders were now empty or deleted. I also had for some reason two files paths to the same music added. So basically I deleted those empty folders and duplicate folders from the library’s list, and voila, my duplicate song issue went away.
I felt kind of stupid after I realized what was going on, so I thought I would share. Plex was still recognizing the empty folders as part of the library and it must be keeping a list somewhere and checking it twice.