With a brief look, I only see one or two pages on your site that are like this. While it is possible it was spammers, I believe this was caused by a period you went through where you installed, imported, uninstalled, reinstalled, reimported, uninstalled, reinstalled etc. I see that existing tagged content is not removed when VaultWiki is uninstalled, so if you reinstall later, you will eventually get an ID that matches one that had tags before (especially for sites that create different content each re-install). So the problem here is that tags on wiki content are not deleted when uninstalling.
Unfortunately there would be no way for a script to tell the difference whether a page had the tags added manually or had the tags inherited from a previous installation, since the underlying bug has no association to your current content in a meaningful way. The only way would be for a human to notice that the tags don't belong, or to remove all tags.
Confirmed due to the uninstall issue.