Summary
When pushing a payment through Stripe and the the customer's credit card is on file, select that card from the bottom of the list box to make the payment.
Key Points
For Payment Method don't select 'Credit Card', you won't get paid
Select the card on file at the bottom of the drop-down list
Finding other misapplied 'Credit Card' payments and fixing them
Credit card is a generic "credit card" payment method that can be used if you have an external credit card processor. FYI, iOS auto-selects the card on file. Android does not.
If you think it's possible other Stripe payments were misapplied:
From the Dashboard, click Sales, click Payments
Click Select payment method...
Click Credit Card
Click Filter
For each line, click Edit on the far right
Click the down arrow to the right of Method, Credit Card
If you see the credit card with the expiration date and the last 4 digits of the card under EFT Transfer as it appears in the example above, click that entryClick Save & Apply
Repeat for the others
Note To prevent this from happening in the future, remove Credit Card from the payment list by following the instructions in Settings - Payment Methods