I have troubles with categories that USED to be populated.
For example, WP shows that 5 posts are in 'Uncategorized' category, but the truth is - none is in there! The posts USED to be there in the beginning, when I didn't provide any category. WP automatically included that category in permalinks. After I finished writing the posts, I changed all of that. Somehow, it remembered that *somewhere*, because everything looks ok in the admin panel.
Even worse, Google webmaster tools is reporting missing links for some posts that direct to /category/uncategorized/.
What's going on here? I have two WP blogs and have exactly the same problems in both of them.