We don’t have much to go on here, but I doubt the seller kept any money from you.
If currency exchange was involved in this sale and there was a fair amount of cash involved, you may have lost something if the exchange rate at the time of the refund differed significantly from the exchange rate at the time of purchase.
What I think is more likely, however, is that you were dealing with a US or UK seller who was using (possibly unknowingly) an eBay international shipping intermediary service (either eBay International Shipping or the Global Shipping Program). Part of the shipping charges for that service are paid to eBay. Sometimes customs-related charges are, too. The seller never sees those funds and they’re not the seller’s to refund.
If you bought from a seller using one of these services, eBay usually automatically refunds what you paid them if you have eBay mediate the refund through a claim through the Money Back Guarantee process. Since it appears that the seller refunded you directly, this didn’t happen. Contacting customer service is probably your best next step . The online chat options are regarded as better than the phone options.
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