Contact eBay and ask them. They can hopefully identify the duplicate payment and credit it back to your eBay seller account, so you will pay less next month.
I don't understand though, why you had to initiate payment of your fees? - mine are taken automatically from my bank account every month. They email me a few days beforehand to tell me how much my last month's fees are, then the fees are taken on a variable direct debit. You shouldn't have to initiate any extra fees yourself?