Did you run the sale with a Square reader synced to your Etsy shop? This will show as a sale in your shop. You will pay the $.20 listing fee, and the 3.5% CC processing fee, but not Etsy's 6.5% transaction fee. Otherwise, you shouldn't see this in your shop - the money should not go through your Etsy shop, and therefore there wouldn't be a way to refund. Not sure how you would refund if necessary to get back the other fees, or if you can, as I don't sync my Square to my Etsy. Most people that do, do it either to keep track of inventory (I do mine manually when at shows) or to get some initial sales when first starting (I have enough sales, I don't need to pay $.20/sale to inflate that number).
I have seen it glitch and sometimes in-person sales don't show up immediately. If you have your Etsy synced to your Square but did not make a sale today, it could have been from months ago and they're just getting caught up.
If you did not sync you Square to your Etsy and have no idea what I'm talking about at all, then you need to get in touch with customer service.
