There are dozens of reports in the Google Webmaster Verification Help section from disgruntled webmasters where they cannot verify their web sites with Google Webmaster Tools.
Jonathan Simon and other Googlers are replying to webmasters that this is a bug and will be fixed soon. In one Google Webmaster Help thread, Jonathan said:
Our verification service has been experiencing intermittent issues today. Please retry verifying your site and post back here if you're still seeing the same error message.
And Dennis G. from Google said in another Google Webmaster Help thread:
Sorry, we had some server trouble this morning. Service should be returning to normal now.
I hope this is resolved soon, if not already.
Forum discussion at Google Webmaster Verification Help.
