You're using a very old RetroPie version, is there are reason for you to do that ?
Regarding your issue - most likely EmulationStation cannot create any new files, since the filesystem is 97% in use. On Linux, by default, a filesystem will have 5% reserved to the root user to prevent users filling it accidentally (or maliciously).
Run EmulationStation manually, then exit (via the menu or F4). Check the log file in ~/.emulationstation/es_log.txt and see if any errors occur when exiting (like files not being able to be created, etc.).

I already try this and the result is the problem returning when I add a new game to favorites.

Yesterday I do some tests and the problem occur with Snes, Megadrive and Nes gamelist.xml. I don’t know the the reason and not see any difference between the files.

Ok, I seem to have figured this out by installing WinSCP, navigating to the files listed in the error messages, deleting them, and then running the scraper to regenerate the files. Now to sort out the bluetooth issue....

@safesinger gamelist file is at /home/pi/.emulationstation/gamelists/<platform>/gamelist.xml or /home/pi/RetroPie/roms/<platform>/gamelist.xml.

@BuZz said in Not finding ROMs in certain SubDirectories:

subfolders are not supported when using gamelists afaik.

Do gamelists house the database-esque lists for every emulators ROMs? (I really know nothing about them to be truthful...just assumed if games weren't showing up I could try and delete the gamelist so it can be rebuilt)

All I know is I have ROM's for NES, SNES, Genesis, and now N64, complete with subfolders. Don't know if deleting the gamelists, or rebuilding all those packages fixed it but it's working so I'm happy.