Before you regulate your inventory with a completed stock count it's is extremely important to consider delivered shipments that have not been invoiced yet. 

If you have already delivered a shipment, but have not invoiced it yet, then that piece will be subtracted from the inventory again if you invoice it AFTER your stock count has regulated your inventory.

To avoid this there are 2 options:

1. You can make sure to invoice delivered shipments without an invoice. If you have no invoices waiting to be invoiced after a delivery, then there is no problem
2. If you have shipments that have been delivered but you cannot issue the invoice yet (hold orders or similar) then you have to manually add those pieces on top of the stock count