This message usually populates when information for a "Working" shipment in Stratify no longer matches up with your Seller Central Shipping Queue. For example, there could be a shipment showing in the Working Shipments area of your List>List & Prep page that has been marked as "Shipped" or deleted.
Solution:
To clear this message, try clicking the Sync Shipments button next to Working Shipments before adding the item to your batch once more.
If the error still populates at that point, you may also have to log out of Stratify and then back in for this to clear.