Once an item has been added to a shipment you cannot change the quantity (qty), as that affects the information already sent to Amazon.  This is done so Amazon can determine to which fulfillment center (FC) the item should go.  Amazon uses your qty, in relation to what they already have in stock and where, to determine to which FC to send your items.

To change the qty of the item you need to delete the item from the shipment grid (by right-clicking the item and selecting DELETE) and re-enter it.  After deleting the item and entering the UPC/ASIN/ISBN in the item search field in the upper-left corner the ADD ITEM TO SHIPMENT(S) pop-up will appear.  There you can enter the correct qty.