Symptoms
Customer subscription was placed on credit hold with "Auto Payments" enabled. Why Payment was not created automatically in time?
Cause
Provider enabled automatic payments for customer's payment method after the Invoice has been generated. The setting was not enabled at the moment of the Billing Order and Invoice creation, so the order stuck on "Waiting for Payment" status.
As the result Account and subscription has been put on hold after the Invoice Grace period ended. (This is set in the customer credit terms).
Account was only released from hold when Invoice has been paid manually.