Hi,
It is inclusive, as you understood it. So what you describe would indeed indicate a problem.
Did the product had several categories in its "categories" setting ? Did the product had variants ?
I've looked into it for a bit after your feedback, and I think I know what the problem is. There is a typo in the new code.
Change the line:
foreach($order->cart->order_products as $product) {
to:
foreach($order->cart->products as $product) {
in the file plugins/system/hikashopaffiliate/hikashopaffiliate.php and try again. It should hopefully work fine then.
We'll be including the patch on our end.