One of the more typical questions you find in the Google Webmaster Help forums is why do not search query reports in Google Webmaster Tools look wrong.

In one explanation from a Googler, he explains how the numbers actually work. Google employee, Asaph Zemach, said in the thread:

This may be one of the clearest and most precise answers I have seen to this question. Of course, it is pretty detailed and specific but if you read it a few times, it should make things crystal clear.

Forum discussion at Google Webmaster Help.