This is an issue that's been happening for me ever since I started using Sitewide Tags with WordPress 3.0, and I've just dealt with it all this time. Since I've never seen anyone else complain about this, I suspect it could be something I've done wrong, but here's the issue:
When posts are made in blogs other than the site's main blog, frequently (but not *always*) they are generating duplicate categories in the main blog. For instance, if someone posts an entry with the category "License Requests," the post is added to the tally of all those using the original "License Requests" category, but it also creates a new category with the same name. This happens over and over, not with all categories, but with specific ones repeatedly. If I don't delete them on a weekly basis, I eventually end up with several pages worth of the same category in my list of categories on the main site. Again, this only seems to happen with certain categories, and it happens with those every time. Others seem entirely unaffected.
It's not a fatal issue, which is why I've never brought it up before, but it is a bit of a pain to maintain. Has anyone heard of this happening before? Any clue as to what's gone wrong?