Just message the seller and describe the problems you found, and ask how he would like to deal with it. Let him know you feel the lens was not as described. Be nice about it and a good seller will be reasonable and try to come to a solution. There are a lot of sellers on ebay that know nothing about the lenses they are selling so he may not have realized the issues. Ask if he is willing to pay return shipping and give a full refund, or alternatively give a partial refund. If the price wasn't very high it can be cheaper for the seller to give a partial refund than to pay return shipping and give a full refund. I'm not sure how many people bid on the auction and so forth, but had the problems been described, the lens would most likely have sold for less (possibly a lot less). Lenses with damage like that tend to sell very cheap, often not much more than cost of shipping. You may have paid more to win it than if the lens had been described properly and a partial refund is a fair solution here if it works for you. That is assuming the circumstances of the auction are like I am guessing (other bidders etc), but you haven't told us how much you paid etc.
I would also try to photograph the damage, and try focusing on the inside elements and take pics too. shine a flash light across the rear of the lens at an angle to see what you get (and shine the flash light across the back when you photograph it too). Take the photos from the front.
This damage was deep inside a 28-200mm lens that I recently bought. It kind of looked like dust and I didn't really know it was fungus till zooming in on photos. It was mainly noticeable at 200mm (at some other distances you couldn't really see it), and was not very visible without some glare from light. The very first thing I do when I get a lens (after looking for obvious scratches), is aim it very near but not right at a bright ceiling light and look through the front of the lens (and zoom it if it is a zoom). Thats how you find stuff like this.
http://www.pbase.com/richardh/sigma_super_fungus
Click a picture, scroll down to the bottom, and click original and you will see what looked like dust to the naked eye.