If what ixian says is true, that “If they follow an affiliate link this may show as click on your affiliate backend” theoretically the way to solve this would be to add a no-follow tag on each of your affiliate links.
By adding the no-follow tag, that may stop stats looking disproportionate.
I personally would go a step further by creating event tracking in GA to see what is (or isn’t) being clicked.
I think that will help you to determine the sign-up rate of that partner too.
V