We got a message in WMT entitled "Googlebot found an extremely high number of URLs on your site".
It was a useful message, because we'd inadvertently created million pages in a section. We got the message in December last year, and then got a subsequent message almost exactly a month later in Jan, and then in Feb.
We then removed these URLs (301-ing them to a correct URL) and removing any links pointing to the URLs internally (they don't have any external links pointing to them).
This worked, because we didn't get the message from Google in WMT in March.
Then today (another month on to the day) we get the same message again - and the sample URLs it has listed are the same ones as before! They are no longer on the site, there are no links pointing to these pages, and they still 301 redirect to other URLs.
So it looks like WMT has dropped back to old data and that's triggered this message.
Funnily enough, we also have had messages for the 'unnatural links', and the number of these unnatural links had dropped (as some were removed), but since then it's increased and the list is showing sites linking to us that don't actually link to us any more.
Does this suggest that Google has some data issues in WMT, or does this go further and relates to the data Google uses for indexing and ranking? Anyone else seen this?