A thread at Google Webmaster Help has a confirmed report of a bug with verifying certain sites in Google Webmaster Tools.
The issue was reported by the webmaster of http://nhschoicespreview.nhs.uk/. The domain would not verify.
Googler, Dennis G., who is the man behind verifying websites in Webmaster Tools, said:
It looks like you found a bug in our code. It currently does not believe that nhs.uk is a valid domain. We'll get a fix out soon. Sorry for the inconvenience.
I am not sure if this is more widespread than a single domain, but I suspect so. I just enjoy reporting these very advanced topics.
Forum discussion at Google Webmaster Help.