How can I issue a refund? #

Open the settings drawer and select Transaction History.  Tap the transaction you want to refund and, if you are an Admin or Owner, you will see an option to issue a refund or resend the receipt.

Can I issue a refund to a different card than the one my customer used to purchase the item? #

No.  Refunds will only go back to the card used to purchase the item.

I am usually able to refund each item in my order.  But, for some reason this time I am only able to refund specific amounts.  Do you know why that would happen? #

Most likely, your customer used a prepaid card to pay for the original transaction and a single card does not have sufficient funds to cover the entire amount and additional payment was required.  In that case, you can only refund the amount charged to each card.

Can I use Quick Refund to refund transactions done in Inventory Mode?

No. It can only be used for Quick Mode transactions.

Reference Site: https://help.clover.com/faq/clover-go-refunds-faqs/