There was an issue where some movie extras could have multiple (thousands) of database entries. This was fixed in 1.25.4.5487. Plex removes a portion of the entries during startup and nightly maintenance. In the worst cases it can take weeks to completely clean things out. The process can be forced by optimizing the database, but the system will be non-responsive until finished.
I think you ran into the cleanup process. Your server was running normally when you shut it down, removing metadata for a featurette (looks like one for Wreck It Ralph).
There are 2649 entries in Plex Media Server.1.log for destroying metadata for Featurette - Rich Moore, and they all have different item numbers. This is why I think you’re running into the problem mentioned above. The process started at 06:17 and was still in process when you shutdown Plex at 09:26.
This thread has additional details from identifying the problem to issuing a fix.
From Plex Media Server.1.log:
Feb 19, 2022 06:17:10.420 [0x70000356b000] DEBUG - Destroying metadata item 11521 (Featurette - Rich Moore)
....
Feb 19, 2022 09:26:09.331 [0x7000034e8000] DEBUG - Ordered to stop server.
Feb 19, 2022 09:26:09.331 [0x7000033e2000] DEBUG - Stopping server...
...
Feb 19, 2022 09:26:09.398 [0x70000356b000] DEBUG - Destroying metadata item 198934 (Featurette - Rich Moore)
Plex should eventually clean things up itself over time. You just have to let it run.
You can force the issue by manually optimizing the database.
The manual optimization will take a long time - tens of minutes or longer (as referenced in the other thread).
The system will be non-responsive while this happens, so plan accordingly (when you will not be streaming for awhile).
Go to Settings → Server_Name → Troubleshooting
Select Optimize Database.
