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.
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.

Comments:
No Name
02/25/2010 12:08 am
My Site listing has been incorrect for months.
No Name
02/25/2010 05:31 am
Google has already provided so many functions and services to it's users.This one is also great that now this service is here for the users.
Jim
03/11/2010 02:50 pm
Its a black art
arif
08/28/2010 11:59 pm
I have this website. In google webmaster tools, the submitted urls is 12 and the indexed url is 0. also only one page comes in google search. where am i making the mistake?