The issue happening in http://irelyserver1.com/irelyi21sco 

Steps :

1. Create Sales and Purchase Contract using the same item =sue reg White crystal and quantity = 100
2. Create Inbound shipment using the purchase contract
3. Create Inventory Receipt for the Inbound Shipment
   1. The IR should have 2 Lot numbers with qty = 50 each
4. save and Post 
5. Create Outbound Shipment using the Sale contract with source type = Pick Lot
   1. The Lot number used here are the Lot numbers created earlier
   2. make sure Qty = 50
6. Save and Post 
7. Create Invoice 
8. Save
9. click on the print button

When printing the  invoice it is showing double entry in the print . please see the below screen shots.