Well, affiliate programs are known to under report. Plus, some international visitors might not apply for the offer and so on. It would have been better to have a separate click counter in between.
I second this. You always want a way to track your actual clickthroughs so you can compare to your affiliate stats. If you're doing enough volume you can sometimes be credited for leads/sales that your affiliate network missed, but only if you can provide them with your own tracked numbers. And really only if the network values your traffic.