Ran into an odd bug this morning and just curious if anyone else has run into this. I have several tv episodes that are flagged as having multiple copies but there is only one file. If I replace the file with a new version it does correct the problem. Forcing a rescan, analyze, refresh don’t appear to have any effect on getting it to recognize there is really only one file present.
Version 1.6.1.3722
CentOS6
I’ve seen that before but it never lasted for very long. That is I would see the duplicate indication then sometime one to twelve hours later (at most a day) the indicator would go away.
It never impacted playback. That is if I tried to play the file showed as a duplicate it played just fine and got a correct watched status afterward. I have started just ignoring it on the rare times it happens.
It probably should be considered a bug but I just think of it as cosmetic glitch. I have found that this is one issue that I only notice if I actually look for it.
It definitely isn’t affecting playback, it was just an odd thing to see.
Have you tried emptying the trash on the libraries, I’ve run into similar when a movie or TV episode is replaced with a better copy or sometimes when reorganizing.
If you have “Empty trash automatically after every scan” enabled (Settings > Server > Library) and the “Library update interval” is set to daily you may see the indicators hang around for a day as @Elijah_Baley mentioned.
If you are using Sonarr or Radarr, both can communicate with Plex and help alleviate false duplicate indicators.
My mothers PMS has this issue too. out of a couple hundred movies, maybe 4 or 5 show up as duplicates even though they are both pointing to the same file and location. Her system has been that way for many, many months now. 
I’ve been getting this quite frequently, lately. Episodes that aren’t upgraded or anything show up as duplicates with the same path…
When i make changes to the SSD cache i usually get a handfull of false duplicates. i just drag them (or a folder) out of the plex lib to non plex folder, refresh the lib and move them back followed by refresh if its not automatic. Takes only a minute. A refresh by itself does not fix them for me. One of those cosmetic bugs that is really low on their priority i expect and as others stated does not affect playback, just ugly to look at.
