This is a known behavior where apps upgraded from a free Starter plan trial to the Growth plan are paid using the default payment method on file, rather than the credits on the account.
If the invoice has not yet been paid (i.e. if the payment failed), you can downgrade to the free plan and then upgrade directly to the Growth plan, bypassing the free trial. The credits should then be applied directly.
If the invoice has been paid already, please reach out to our support team who will be happy to help.