There are a lot of reports lately of issues with Google Webmasters Tools. Issues are fixed but then they return. For example, we have this post reporting 0 crawled pages from October 23; on October 24, we still had individuals leaving comments saying that the problem wasn't fixed. In July, we had a 404 reporting error but it was later fixed. We have reports that Google Webmaster Tools are inaccurately displaying keyword positions among other issues.
In the forums, we have a lot of other reports. One webmaster finds that Google Webmaster Central is showing the title of another website as associated with his site. Hacked? No. Bad coding? No. Google Webmaster Tools? Yes--at least, the evidence in Google Groups and other related reports points to that.
Another forum member says that regardless of what she does, Google gives her the warning that there are "too many URLs for Googlebot" -- even if she uses robots.txt to block off the offending URLs.
Also, earlier this month, WebmasterWorld had a thread about how Google now tells you where your 404 errors are coming from. Many people are happy with this tool but others actually think it's inaccurate.
There's a lot of forum discussion, so here are the links if you want more information: