incrediBILL - 9:27 am on Apr 10, 2013 (gmt 0)
Middle of last year, Google suddenly started sending me warning mails via my Webmaster Tools account, telling me about "possible outages" and that "Googlebot can't access the site". I looked into those, and noticed that Google had found...
The two incidents were probably unrelated because many people were getting those messages last year due to hackers running a big botnet attacking various DNS servers around the globe, most likely Google's, which caused "outages" as Google was unable to crawl the site because DNS wasn't being resolved properly. You may want to check that DNS graph, if they still have it, that showed DNS failures to my server which simply didn't exist as my servers and DNS were up 100% otherwise my multi-peer alarm monitoring service also would've complained about service outages which didn't occur.
What people don't realize is if someone on your circu in a hosting company are under attack then Google probably can't access your server until that DDoS is mitigated and I can give you a bunch of other possible reasons as well which are also likely culprits but hDDoS is the most common reason IMO for that message.
If you're merely having 404, 410 or other results to missing pages then it'll be filed under the proper HTTP result code for the crawler and if you aren't giving the right result codes then you may want to consider fixing the software to properly handle such inquiries.
I've had similar accidents and Google seems to resolve the issues pretty fast once you've gotten everything back to normal and eliminated all the problems.
Good luck with that.