A quick look at your logs and I see the following …
Jan 16, 2022 10:03:59.025 [19760] DEBUG - Looking for path match for [F:\Movies\Taken (2008) {tmdb-8681}\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.025 [14580] DEBUG - Native Scanner: Executed Local Metadata stage in 0.00 sec.
Jan 16, 2022 10:03:59.313 [19760] DEBUG - [MetadataAgent/tv.plex.agents.movie] Found 1 provider matches for 'Taken (2008)'.
Jan 16, 2022 10:03:59.313 [19760] DEBUG - Scanner [Plex Movie]: found cloud match for file 'F:\Movies\Taken (2008) {tmdb-8681}\Taken (2008) {tmdb-8681}.mp4': 'Taken'
Jan 16, 2022 10:03:59.313 [19760] DEBUG - Native Scanner: Executed Cloud Match stage in 0.29 sec.
Jan 16, 2022 10:03:59.313 [19760] DEBUG - Looking for path match for [F:\Movies\Taken (2008) {tmdb-8681}\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.313 [14580] DEBUG - Looking for path match for [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken 2 (2012) - 1080p.mp4]
Jan 16, 2022 10:03:59.314 [18408] DEBUG - Native Scanner: Executed Local Metadata stage in 0.00 sec.
Jan 16, 2022 10:03:59.314 [20248] DEBUG - Activity: updated activity c0f205ad-08d1-48b0-86d8-4e8fa4ad1b60 - completed 0.2% - Scanning Movies
Jan 16, 2022 10:03:59.314 [20248] DEBUG - Scanner: Processing directory F:\Movies\Zootopia (2016) - 1080p (parent: yes)
Jan 16, 2022 10:03:59.314 [14580] DEBUG - Scanner [Plex Movie]: found existing media id 5121
Jan 16, 2022 10:03:59.314 [14580] DEBUG - Native Scanner: Executed Cloud Match stage in 0.00 sec.
Jan 16, 2022 10:03:59.314 [19760] DEBUG - Checking by hash to see if we can find a match with 36c1743368951e9fc3fe25e96a472cfdff82e09f (display offset: 0, not part -1)
Jan 16, 2022 10:03:59.314 [19760] DEBUG - We found a hash match for [F:\Movies\Taken (2008) {tmdb-8681}\Taken (2008) {tmdb-8681}.mp4] which was [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken (2008) {tmdb-8681}.mp4].
Jan 16, 2022 10:03:59.316 [19760] INFO - Part rename detected [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken (2008) {tmdb-8681}.mp4] was renamed [F:\Movies\Taken (2008) {tmdb-8681}\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.316 [19760] DEBUG - Updating media item 5131, size=1391937186, metadata_item_id=2504
Jan 16, 2022 10:03:59.316 [19760] DEBUG - Updating part with ID=24166 [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.317 [19760] DEBUG - Turbo analysis on modified item 5131 [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.317 [20248] DEBUG - Skipping over directory 'Zootopia (2016) - 1080p', as nothing has changed; removing 1 media items from map.
Jan 16, 2022 10:03:59.317 [20248] DEBUG - Activity: updated activity c0f205ad-08d1-48b0-86d8-4e8fa4ad1b60 - completed 0.3% - Scanning Movies
Jan 16, 2022 10:03:59.317 [20248] DEBUG - Scanner: Processing directory F:\Movies\Zombieland Duology (2009 - 2019) - 1080p (parent: yes)
Jan 16, 2022 10:03:59.317 [19760] DEBUG - Updating media item 5131, size=2783874372, metadata_item_id=2504
Jan 16, 2022 10:03:59.317 [19760] DEBUG - Updating part with ID=24166 [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken (2008) {tmdb-8681}.mp4]
Jan 16, 2022 10:03:59.318 [16876] DEBUG - Media Analyzer: Performing on-the-fly analysis on 1 item.
Jan 16, 2022 10:03:59.318 [20248] DEBUG - Skipping over directory 'Zombieland Duology (2009 - 2019) - 1080p', as nothing has changed; removing 2 media items from map.
Jan 16, 2022 10:03:59.318 [20248] DEBUG - Activity: updated activity c0f205ad-08d1-48b0-86d8-4e8fa4ad1b60 - completed 0.4% - Scanning Movies
Jan 16, 2022 10:03:59.318 [16876] DEBUG - [JobRunner] Job running: set "FFMPEG_EXTERNAL_LIBS=\\\\?\\C\:\\Users\\Thomas\\AppData\\Local\\Plex\ Media\ Server\\Codecs\\fb9eae3-4185-windows-x86\\" & set "X_PLEX_TOKEN=xxxxxxxxxxxxxxxxxxxx" & "D:\Plex Media Server\Plex Media Scanner.exe" --analyze --log-file-suffix " Analysis" --no-thumbs --item 2504
Jan 16, 2022 10:03:59.318 [20248] DEBUG - Scanner: Processing directory F:\Movies\Zero Dark Thirty (2012) - 1080p (parent: yes)
Jan 16, 2022 10:03:59.318 [19760] DEBUG - Native Scanner: Executed Add to Database stage in 0.00 sec.
Jan 16, 2022 10:03:59.318 [19760] DEBUG - Native Scanner: Executed Media Analysis stage in 0.00 sec.
Jan 16, 2022 10:03:59.318 [19760] DEBUG - Looking for path match for [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken 2 (2012) - 1080p.mp4]
Jan 16, 2022 10:03:59.318 [14580] DEBUG - Looking for path match for [F:\Movies\Taken Trilogy (2008 - 2014) - 1080p\Taken 3 (2014) - 1080p.mp4]
I think the Taken Trilogy (2008 - 2014) - 1080p stuff is messing it all up for you. Put all those movies under F:\Movies as from looking in your logs I believe this is the library path you used in plex and remove the Taken Trilogy (2008 - 2014) - 1080p.
This is how I have my versions of these movies …
/data/32TB-Media-Server/Movies/Taken 2 (2012) {tmdb-82675}/Taken 2 (2012).mp4
/data/32TB-Media-Server/Movies/Taken 3 (2014) {tmdb-260346}/Taken 3 (2014).mp4
/data/32TB-Media-Server/Movies/Taken (2008) {tmdb-8681}/Taken (2008).mp4