If customers run out of credits & can’t join class off the waitlist, shouldn’t the customer’s card on file be charged?

The customer's card on file will not be auto-charged in this case unless a special General setting is enabled.

In Settings > General Setup, near the bottom under the section titled Unpaid Class Bookings you can enable "Automatically settle (pay for) unpaid bookings before a class starts" & subsequent " Charge payment method on file if no membership is found".