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Hi-- I know this thread is a few months old, but I'm having the same problem: mysterious subjects Marvin adds to books that aren't in the tags field in Calibre, or anywhere easy to get at. I haven't seen a solution posted anywhere else, but I have found a thing that works for me. It might be a bit of a bodge, so if you want to try this, I ***highly recommend*** that you back up your library first!
Okay, so where are those tags coming from: they are, as far as I can tell, embedded in the book itself, and that's whence Marvin is pulling them. These tags don't show up as tags in Calibre, so that's why you can't get rid of them in metadata edit. You can get rid of them, though: Calibre has a feature called 'Polish Books' which will, among other things, strip them out, leaving only the tags you have assigned in Tags. So, step by stem:
First, get your own tags in your Calibre library to be how you want them. If you use tags you have probably already done this.
Next, if you don't have the Polish Books button in your toolbar, go into preferences, toolbars, and enable it. It looks like a little broom.
Go back into your regular view. Select a book or books to edit and push the button. You'll get a number of options with tick boxes beside them. The one you want is 'Update metadata in the book files'. Tick that box, and let it work its magic. Note that if you have selected many books and you have a large library, this could take some time.
Calibre will create an ORIGINAL.EPUB file alongside your modified one (I imagine you can use this to restore the old metadata later, should you ever want to and you don't want to just download it from within metadata edit) but you can, if you need the space, safely delete it (or at least nothing awful happened when I deleted mine, but make sure you have your backup just in case).
Delete the old books from Marvin's library and re-import them, and you should see collections only under your own assigned tags.
This worked for me, anyway-- I hope someone finds it useful.
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