I just spoke with support, and there was indeed an issue: the sign-up flow prompted me to use the Developer.app on macOS, and I purchased a subscription through the App Store there. I then returned to the Apple Developer Program web sign-up page to continue the process, but it asked me to pay again, which I didn't do. This resulted in a failed payment (and then several, since I tried multiple times over few days), leaving my account in an unstable state. The support representative resolved the issue. I think that there is bug in the enroll flow (a race between Developer.app flow and web flow)

Exactly the same problem here: I’ve been charged I received the invoice & subscription is visible on Apple Store But in my Apple Developer account settings, I’m being asked to pay: "To continue your enrollment, purchase your subscription now" where I have to pay again Ticket opened, but no response so far