I assume you are using the GP manufacturing modules with Manufacturing Orders. You were vague. Also, it would help to know what version you are on.
Please take the following steps to test where the extra costs are coming from. On the next MO with outsourced costs, before receiving the PO for the outsourced work, check the MO Variance Inquiry and record the amount of money in WIP for the Outsourced Costs. Receive the PO and post the receipt, then check this value again. This is the first step, to ensure that the PO is being received correctly.
Next, is the outsourced service listed in the BOM? The parts/services should NOT be in the BOM. If they are, then you are pulling one set of costs from the Outsourced PO Receipt and a second one from the BOM.
Try these and post back.
BTW..we have a good set of books that discusses manufacturing and outsourcing. Product Engineering and Shop Operations, as well as Manufacturing Cost Accounting are great resources.