Certainly smells like a permission problem. I can see these in your log…
Sep 29, 2022 07:33:22.892 [0x7f2184ba2b00] DEBUG - Updating directory 'A Nightmare on Elm Street (1984) {tmdb-377}' (ID 2168) to time 2022-09-28 19:48:17.
...
Sep 29, 2022 07:33:22.940 [0x7f2184ba2b00] DEBUG - Activity: updated activity 2fc2a358-0db5-4c7a-bfb5-d2ba0a5071b4 - completed 100.0% - Scanning Movies
so you can see it finds the folder and the scanning completed but I cannot see any mention of the file itself.
I can also see from your logs that Star Trek - Lower Decks - s03e06 - Hear All, Trust Nothing.mkv was successfully found and added.
Sep 29, 2022 02:21:34.447 [0x7f2183642b00] DEBUG - [MetadataAgent/tv.plex.agents.series] Found 1 provider matches for 'Star Trek Lower Decks'.
Sep 29, 2022 02:21:34.447 [0x7f2183642b00] DEBUG - Scanner [Plex TV Series]: found cloud match for file '/volume1/video/tv/Star Trek - Lower Decks/Season 3/Star Trek - Lower Decks - s03e06 - Hear All, Trust Nothing.mkv': 'Star Trek: Lower Decks'
Sep 29, 2022 02:21:34.447 [0x7f2183642b00] DEBUG - Native Scanner: Executed Cloud Match stage in 0.51 sec.
Sep 29, 2022 02:21:34.447 [0x7f2183642b00] DEBUG - Looking for path match for [/volume1/video/tv/Star Trek - Lower Decks/Season 3/Star Trek - Lower Decks - s03e06 - Hear All, Trust Nothing.mkv]
Could you compare the file permissions on that file with the one from the movie and see if there is something different. I don’t use synology myself but it certainly could be some permission related problem. I assume you have done everything called out here → Synology FAQ - Questions, Answers, and a few How-To's - #25 by ChuckPa. There is a final note in that section which might be what you are seeing, so maybe Apply to this folder, sub-folders, and files needs to be done again ?
Outside of all that I suggest when @ChuckPa comes online if he could take a peek 
