I'm not sure if this is specifically a 2.0 bug or not - and to be honest, I have had little time to investigate further - however, since you guys want to catch as many bugs as you can to get 2.0 out soon, I thought I would post this just in case. I have had the counter (for the number of posts in a category, on the front page) go a little weird on me after upgrading. BUT, if I'm not mistaken, it only did so on posts that were imported via FeedWordPress (the RSS Aggregation plugin). If I'm not mistaken, what would happen is that I would delete imported entries, then delete entries created on the WP installation itself - and would end up with a negative number for the number of entries. I think the same thing happened if I would change the category of a post, as well.
Please keep in mind, though, that this may very well be because I have done screwy things, like trying out nightly builds of 1.6, and going back to 1.5, and so forth - and when I have time I am just going to wipe the folder and the database clean and start over - so, this isn't so much of "please help me figure this out" question, rather, just an odd quirk that I thought I would note in case anyone else has experienced this, and if it is indeed a 2.0 bug/issue (however my gut says otherwise).
Other than that, I've had little or no issues so far using the different builds of 2.0. Good luck, and I'm excited about trying it out!