I used to have these problems randomly popping up on me.
Turned out it wasn't a problem with all the missing ones, but somewhere during the update process it came across filenames that contained invalid characters for Plex and that stopped the whole scanning.
Make sure that all your media files that Plex is scanning only contain a-z,A-Z,0-9 and "-" and spaces in the filenames.
This problem has now been solved.
However I have the following problem with NCIS.
For some reason Plex has decided to create random NCIS icons on the TV show Tab for NCIS. I have Season 1 to 12 are OK.
Season 13 is problematic.
It has episodes 1- 15 in the correct folder on Plex.
Episode 16 has its own Icon in Plex
Episodes 17 & 18 Have own Icon in Plex
Episodes 19 & 20 Have own Icon in Plex
Episodes 21 & 22 Have own Icon in Plex
Each season and episode follows the following protocol
\NCIS\Season NN\SSSEEE Episode.Extension
eg
\NCIS\Season 13\S13E01 Stop the Bleeding.mkv
This is the same for every season and episode. As below
@meyerpr said:
I just had the same problem with NCIS S13EP11 and 13. I had to manually match them to get them together with the rest of the ‘regular’ Season 13.
If you name your files S13EP11 it won’t work. Lose the P.
If you use mp4/m4v files, then the embedded title tag in these may contradict your file names. Either delete the embedded metatags or make Plex ignore them by:
Go to Settings - Server - Agents - Shows - TheTVDB
In there, grab the line ‘Local Media Assets’ with your mouse and drag it downwards, so it ends up being at the bottom of the stack of active agents.
Then perform the Plex Dance with the affected episode(s).
Split/Merge should be always the last resort, because the problem tends to repeat itself when further episodes are added.