There is corruption in the file system. With this type of corruption of the name, it is very likely there is other corruption of the file / directory pointers too.
in Token (Kleptomanta)
Nov 21, 2018 19:19:01.192 [0x7f1647bff700] DEBUG - DirectoryBrowser: Decoded [L21udC9NeSBQYXNzcG9ydC9NZWRpYS9WaWRlby9KYXBhbmVzZS@jgqLjg4vjg6E=] to [/mnt/My Passport/Media/Video/Japanese(ਸ\E0\E2\F8\E0]
Nov 21, 2018 19:19:01.194 [0x7f1647bff700] ERROR - Couldn't check for the existence of file "/mnt/My Passport/Media/Video/Japanese(ਸ\E0\E2\F8\E0": boost::filesystem::status: Invalid or incomplete multibyte or wide character: "/mnt/My Passport/Media/Video/Japanese(ਸ\E0\E2\F8\E0"
Nov 21, 2018 19:19:01.194 [0x7f165bffe700] DEBUG - Completed: [127.0.0.1:57848] 200 GET /services/browse/L21udC9NeSBQYXNzcG9ydC9NZWRpYS9WaWRlby9KYXBhbmVzZS@jgqLjg4vjg6E=?includeFiles=1 (5 live) GZIP 2ms 350 bytes (pipelined: 8)
Nov 21, 2018 19:19:03.319 [0x7f165c7ff700] DEBUG - Auth: authenticated user 1
Some of what it finds is valid.
Nov 21, 2018 14:45:53.409 [0x7f35c8bf7700] DEBUG - Item 14849 (リトルウィッチアカデミア (2017) - 18 - 空中大戦争スタンシップ) Scanning metadata graphic elements in XML file ""/Info.xml
Nov 21, 2018 14:45:53.409 [0x7f35c8bf7700] DEBUG - Item 14849 (リトルウィッチアカデミア (2017) - 18 - 空中大戦争スタンシップ) Scanning metadata graphic elements in XML file ""/Info.xml
Nov 21, 2018 14:45:53.412 [0x7f35cc3fe700] DEBUG - Request: [127.0.0.1:41934 (Loopback)] GET /library/metadata/14850/tree (19 live) GZIP Signed-in Token (Kleptomanta)
Nov 21, 2018 14:45:53.415 [0x7f35e8fff700] DEBUG - Completed: [127.0.0.1:41934] 200 GET /library/metadata/14850/tree (18 live) GZIP 3ms 770 bytes
Nov 21, 2018 14:45:53.419 [0x7f35c8bf7700] DEBUG - Loading information from media bundle for part ID 16768 from "/var/lib/plexmediaserver/Library/Application
I presume this is Anime ?
The matter is further compromised by the scanner only seeing bad names here.
Nov 21, 2018 14:43:00.525 [0x7f35e8fff700] DEBUG - Completed: [127.0.0.1:51520] 200 GET /:/metadata/updateProgressMessage?message=Scanning%20%E3%82%BD%E3%83%BC%E3%83%89%E3%82%A2%E3%83%BC%E3%83%88%E3%83%BB%E3%82%AA%E3%83%B3%E3%83%A9%E3%82%A4%E3%83%B3II%20[1080P] (29 live) GZIP 0ms 166 bytes
Nov 21, 2018 14:43:00.528 [0x7f35da3fc700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/.plexignore
Nov 21, 2018 14:43:00.530 [0x7f35d73f6700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCED 1 [BD 1080p FLAC] [D4B9767E].mkv
Nov 21, 2018 14:43:00.531 [0x7f35db3fe700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCED 2 [BD 1080p FLAC] [AF7ACCDA].mkv
Nov 21, 2018 14:43:00.533 [0x7f35d63f4700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCED 3 [BD 1080p FLAC] [68B9C079].mkv
Nov 21, 2018 14:43:00.535 [0x7f35dbbff700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCED 4 [BD 1080p FLAC] [2D8F2BAA].mkv
Nov 21, 2018 14:43:00.536 [0x7f35d93fa700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCOP 1 [BD 1080p FLAC] [E3F06E4A].mkv
Nov 21, 2018 14:43:00.537 [0x7f35d23fc700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCOP 2 [BD 1080p FLAC] [E94FF177].mkv
Nov 21, 2018 14:43:00.539 [0x7f35d33fe700] DEBUG - [Scanners.bundle] Removing file due to plexignore rule (.*\Z(?ms)): /mnt/My Passport/Media/Video/Japanese/���������/������������������������������������II [1080P]/NC/[SallySubs] Sword Art Online II - NCOP 3 [BD 1080p FLAC] [CA66989F].mkv
Nov 21, 2018 14:43:00.541 [0x7f35d9bfb700] DEBUG - Request: [127.0.0.1:51538 (Loopback)] GET /:/metadata/updateProgressMessage?message=Scanning%20%E3%82%BD%E3%83%BC%E3%83%89%E3%82%A2%E3%83%BC%E3%83%88%E3%83%BB%E3%82%AA%E3%83%B3%E3%83%A9%E3%82%A4%E3%83%B3II%20[1080P]%2FNC (29 live) GZIP Signed-in Token (Kleptomanta)
Nov 21, 2018 14:43:00.541 [0x7f35e8fff700] DEBUG - Completed: [127.0.0.1:51538] 200 GET /:/metadata/updateProgressMessage
Notice the directory name characters. This is more indicaton of where your problem is.
The .plexignore is showing us the name of the directory (where the ignore begins) is already problematic.
I cannot be more specific with this level of data.