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The obvious explanation is that the credit card is being used as the payment method on some other Github account than the one that the author checked.
A quick look at the source code reveals they are using Stripe, so they probably don't store any payment cards.

I guess that they send your info to Stripe as the default recurring payment method, and it keeps billing until you remove the service.

You were charged for something you did not buy and your conclusion is that GitHub is storing deleted cards?

1. Might you have a long forgotten GitHub account? 2. Have you checked that the card isn't compromised?

Instead of writing an uninformed and clickbait article that plugs author’s startup at the end, a simple email to GH support would have sufficed.
This is a question for github customer support, not medium.