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:
We recently had a small issue with the indexed URL counts in Webmaster Tools for some sites. This should be resolved now and back to normal for most sites that experienced this issue (it might take a day or two to catch up everywhere).
Thanks for your patience!
So if you feel your index count is wrong, it certainly may be wrong.
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.