I've noticed the "wrong thumbnail" problem on one of my albums too. But as far as I can tell, it looks like maybe a caching issue. (Try this: move or copy a "wrong" thumbnail to a new filename, and then access it through the web. For me, it showed the right thumbnail then, insinuating that somehow the "wrong" image was just a cached copy (or something).
As for the thumbnails not being deleted, that'd be a bug. It's supposed to delete them, so I'll have to check that one out.
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