I'm a bit confused what exactly you did so unsure if there is a bug.
How were you running this file through the file organiser if it was hidden from the main panel?
Not entirely sure myself. It didn't appear before. I just noticed after I updated to one of the 3.6 builds (it could've happened before the version I mentioned in the first post).
Like I said, when I go into the preferences and setup the file organisation, the file would appear right at the top of the list - along with any other files that needed to be reorganised. Alternatively, using ctrl-R to bring up the file organiser, the file wouldn't appear. I don't know why just this one track stuck around - the remaining album tracks got deleted from the library, regardless of being hidden.
I got it sorted now (unchecked it in duplicates so it wasn't hidden, and finally deleted from the library), so I doubt it's worth you burning any calories looking into it further