By default, when Subscribe Pro groups multiple subscriptions together into a single order, if one subscription fails for some reason, such as a product being out of stock), the entire order will fail and each subscription will include an error saying that one of the products was out of stock.
A configuration option is available that changes this behavior. This can be found under System > Configuration in the Ordering Settings tab. This setting is called Partial Order Mode, and it has two options: Require all subscriptions to be successfully ordered (default), and Allow partial orders. When this is set to Allow Partial Orders, if a subscription in a group were to fail in the scenario above, only that one subscription would be marked as failed, and our system would continue to attempt to place a recurring order with the rest of the items.