Hank here from Shopify.
Sorry to hear you are having issues with purchasing a domain, it certainly sounds like there is some form of disconnection, as it seems to be automatically failing, and that is why the refunded amount is there for you.
Some domains are unable to be hosted on Shopify so that could be the issue you are facing perhaps? Premium domain names, for instance, are unable to be supported on Shopify, so that could be what is happening. You would be left with an error message of something like the below.
You can still try to purchase this domain through another registrar, as it is not compatible with the Shopify server at this time.
Let me know if this works for you, or if you have any other questions, and I'd be happy to help!
All the best,