BOM Cost Report Calc Problem

Has anyone else run into a problem with the bill of materials cost report not calculating costs properly when a quantity of a component of an assembly is anything less than 1 per assembly? We have part A which has components B,C,D, etc… component D (shipping tray) is only .001 qty per assembly A since many assemblies can fit onto a tray. On the BOM Cost report it shows that the qty is only .001 but it shows the total cost of the tray. By the end of the report it shows 1 assembly costs way more than it should because its using the total cost for the tray, not .001 of the cost. This shipping tray is used with multiple assemblies we have and the quantity per assembly is different. Can Epicor BOM Cost report not account for this? Do we just have this setup wrong? It seems like the BOM Cost report should show only .001 of the total cost of the shipping tray