Hello,
I have the same issue. Having 404 errors |(over 500) for un-exacting uls and lot of tags.
It started after upgrading my site, and urls just disappeared. Checking with webmaster tools for the "linked from" there is a big list. But clicking on each link - some do not exist and going to error page and other just go to unrelated pages.
Big mess that I don't know how to fix.
Appreciate any help