Tried this out with a movie that had 180p and 480p versions in the folder. Used sub folders as suggested by the docs and the extras where duplicated in the web view. I removed the 480p version from the folder and the duplicates were removed. Is this expected?
Would you mind sharing the exact folder structure / file names you were using? What exactly do you mean by the extras being duplicated (maybe a screenshot)?
Then I removed the SD version with its SUB files and scanned the library again. The duplicated extra files were removed.
I then decided to remuxed the MP4 and Subs for the SD version into an MKV. Added that file scanned and everything worked as expected. No duplicates with the extras. I have a bunch of extra material that I’ve been sitting on. I might try a few more titles to see if I can replicate the issue.