Can you share some screenshots on the Prod. BOM an Routing, as well as the the Work Center/Machine Center cards involved? Then it would be easier to determine the cause and provide a solution
The problem is the Backward flushing on the routings. When you finish the order, the backward routings will be posted, and since there is arouting link code as well, the linked Components will be consumed. Change the Machine centers to Manual flushing. Backward flushing is useful if you have some cost that you want to add to the output without users having to post it, such as indirect costs, paint, glue or other.