Accodring to their editorial guidelines, it says "If you are an affiliate and are paid to send traffic to another site or a distributor, you must identify yourself as an affiliate or a distributor in your ad text.".
How do they distinguish between tracking urls, or affiilate urls?
Most affiliate URLs are pretty obvious due to the fact that they are from one of the major affiliate programs. I believe the editors do check the website when they check your ad (and sooner or later they will check your ad) but occationally an innocent tracking URL gets mislabled as an affiliate. All you need to do in this case, is contact adwords and let them know that you are not an affiliate and make sure you ask them to make note of that on your account so that it does not happen again.
The affiliate tags are usually embedded into the URL itself, so for the major affiliates (like the one I belong to), Google should have a fairly easy time determining which URLs are affiliates and which aren't.
If you ARE an affiliate, you should note that fact in the ad copy itself with either the word affiliate or an abbreviation thereof. :)