So the accused were placing an unrelated widget on other people's sites and adding the eBay cookie as part of the payload. The user never actually was directed to eBay.
So say eBay notices they are serving 1 million cookies a month to users, but only have 50,000 visitors relating to those people on their homepage. That's how they know this was cookie stuffing and not legitimate traffic.
I don't think this description is accurate. It makes no sense for an invisible iframe to display the entire ebay homepage to the user - people would notice 100's of server connections and an extra 1MB download for a page view. More likely they found the one Javascript file on ebay that creates the cookie, and ONLY loads that Javascript.
Well, I know that's how _lots_ of people did it in 2003/2004. The guys I hang out with (ahem...) were some of them. In the more shady parts of the internet it's actually still quite common today. Nobody notices anything.
So say eBay notices they are serving 1 million cookies a month to users, but only have 50,000 visitors relating to those people on their homepage. That's how they know this was cookie stuffing and not legitimate traffic.