It sounds like they are being kind to their vendors. If they make a purchase for $1000 then return half for credit of $500, it is fair to apply the 2% to both invoice and credit, resulting in discount of $10, not $20.

Of course, this would work just as well if credits were immediately applied to the related invoices resulting in a lower amount due. But the timing may not work since they are paying the invoices quickly and the credits may lag behind.