Currently all items are brought into ShipStation regardless of whether or not they are already fulfilled on Shopify. We often issue refunds immediately following a customer purchase due to customer error, at which point we mark the item as fulfilled in Shopify to prevent us from shipping product that has been refunded.
ShipStation shows all items on an order regardless of if they are fulfilled on Shopify or not, and prints them all on the packing slip. Even 'Syncing' after order changes does not correct this. I have to imagine others must be facing this issue and running the risk of shipping product that has been refunded!