lorax - 5:47 pm on Mar 11, 2013 (gmt 0)
It could if you don't take steps to exclude the affiliate pages from the indexes. You'd keep the top level urls that point to the products without the /aff/###/ so they could be indexed by the bots. Then any of the affiliate pages could be noindex. Since I'm not really sure how you're setup nor the relationship with your affiliates and how the site is being used, this is all hypothetical.