The AdWords Blog posted a report of how some of the independent third party click fraud reports published are exaggerating the clickfraud numbers. Google says they have seen some reports that show "1.5 times the number of clicks in our logs."
Google published a larger paper on the issue. They summarize "two main points" of the larger paper as being,
1." Fictitious ad clicks because of mischaracterizing events."
Click fraud consultants don’t count actual ad clicks. Rather, they use a number of other signals, including counting visits to a particular webpage. Hence, the consultants count page reloads and subsequent visits on an advertiser’s site as multiple clicks on the advertiser’s Google ad. This generates fictitious ad clicks in the consultant’s reports.
2. "Fictitious ad clicks due to conflation across advertisers and ad networks," where cookie issues confuse Yahoo! clicks with Google clicks.