Following circumstances may lead to some value shown in the inventory without quantity:
1. Editing the purchase price after the sale/transfer is recorded for the item.
2. Allocating cost to an item which has no inventory / editing the costs allocated after the inventory is sold/transferred.
Solution:
Option 1. Run 'All transactions' report for the product (also keep the lot no if you are doing the lot tracking) and find out the goods issue(s) where unit cost is not correct. Update the status of all such goods issues to 'not shipped' and mark them as 'shipped' again. This will recalculate the unit cost considering the balance value remaining for the product. Now value of the product will get consumed.
OR
Option 2. Do the stock adjustments only to the value. To know more on stock adjustments refer here: https://arkainventory.freshdesk.com/support/solutions/articles/48001192064-making-adjustment-to-the-stock