I contacted support via Apple Developer page > support > contact us. They refunded the extra charge. Took about 6 hours for the reply. It will take the usual upto ~15 days for banks to process it, but I got the email with the refund invoice/credit pdf.

I ran into the same issue. I enrolled and got the subscription on Apple Developer app on iPhone. But after payment, the app shows "account cannot be enrolled via mobile app" and ask to enroll via web. I did, and I got charged again. How do I refund the subscription from app store? https://reportaproblem.apple.com/ doesn't let me refund and says I have no products eligible for refunds. Who/where do I contact to refund apple developer program double charge?