If you have a Shopify or a WooCommerce store, then Refersion has tools to help negate the affiliate's commission for returned orders. This way you are not paying affiliates a commission for orders that were returned by your customers. You can read more about configuring this tool for your Shopify store or your WooCommerce store
If you are not on Shopify or WooCommerce, then you can always issue a Manual Credit to adjust for the return.
For all business owners, regardless of e-commerce platform, it's best to hold all affiliate payments until the end of your return period. This way you have time to review all commissions earned and then pay only the ones that are valid orders that have not been returned or canceled. Some common affiliate payment schedules are once a month or once every 45 days to accommodate a 30 day return period.