When a customer wants to return a single product within an order, the best way to go about it is to process the refund for the amount of the product (to do so, please see the following article: http://help.crystalcommerce.com/faqs-and-troubleshooting/how-to-use-crystalcommerce/orders-how-to-refund-an-order) then you can locate the product in question on the Inventory > Products screen and manually adjust the Quantity to the correct amount.

To process the refund, first open the order by clicking on the order ID from within your Orders tab. Once the order is open in it's own screen, new options appear. Here, click on the "..." button in the upper right hand side of the screen, the click "Process Refund". In the box that appears below, you can select the refund type, refund amount, and enter in a reason. Finally, Click "Give Refund".

Next, head over to the Inventory => Products tab, search for the product that is being refunded, and add the quantity back into stock. Hit "Save" when complete!
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​It is important to not click the red X icon next to products on the order, as it will cause discrepancies within your inventory.   In circumstances such as this, it is best to manually adjust the Qty of the product in question to the correct amount and notate your records.
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To learn how to process a return for an entire order, please see the following article: http://help.crystalcommerce.com/faqs-and-troubleshooting/how-to-use-crystalcommerce/accepting-returns-for-an-entire-order
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