There was a brief time where Google Webmaster Tools was reporting the wrong number of indexed URLs for a web site. JohnMu from Google confirmed the issue in at least two Google Webmaster Help threads. He said:

So if you feel your index count is wrong, it certainly may be wrong.

Forum discussion at Google Webmaster Help.

Note: I just landed in Jerusalem, after an 11 hour flight. I am typing as fast as I can, so please excuse typos, grammar and any non-sense.