Hello,
This is by design:
In versions 3.0.0 and later of the payment gateway, which are designed to work with version 6.0.0 of the plugin, the funds are simply subtracted from the user’s balance, with a credit transaction. Since the user will have deposited funds to gain that balance, any funds subtracted from their balance simply belongs to the site.
Also see the glossary definitions for “Hot wallet balance” and “User balance” for more details on this.
It’s best to think of it with an example. Say user A deposits 1 Litecoin. Then, their LTC balance is 1, and the site’s hot wallet balance for LTC increases by 1. Then, user A purchases a product that costs 0.5 LTC and checks out. Now the user’s balance is 0.5 LTC, but the hot wallet balance remains on the site, and can be withdrawn to an external wallet using the Cold Storage tool.
In case of a refund, the user’s balance is increased again and the order is marked as refunded. Nothing else changes. You can see an example of a checkout transaction and a refund transaction here: 
(In versions prior to 3.0.0, the WooCommerce payment gateway did indeed transfer funds from the buyer to a designated admin account. This is no longer the case.)
Hope this is clear, please let me know if it’s not, or if you have any more questions.
with regards,
Alex