@webtoffeesupport I have the same issue. The first payment order generated by Woocommerce Subscriptions has the correct sequential order number, but the recurring order does not. The recurring order appears as a “related order” on the order details page. Version 1.6.5.
This issue is with Woocommerce core, not the Subscriptions plugin, which is working correctly. Woocommerce itself is displaying the wrong order price, as the payment is scheduled for later.