As the merchant, you reserve the right to reject a commission payout to an affiliate. However, it is important that you only do this in a case of fraud. If an affiliate is attempting to claim credit for a self referral or other fraudulent order, rejecting the payout is a good idea, as well as deleting the affiliate's account. However, if the payout is for a legitimate order, it is important that you pay the affiliate their owed commission as soon as possible.
If you are unsure whether an order is legitimate or not, read here on protecting against fraud.