Please check what your Default Close Calculation Option is. (Microsoft Dynamics GP menu >> Tools >> Setup >> Manufacturing >> System Defaults >> Manufacturing Orders)
If the manufacturing order end quantity doesn’t match the total received from the order and you’re closing a manufacturing order for a standard cost finished good item and you need choose the Total Quantity Received calculation option.
Also please check the component in bill of material. If the component has a fixed quantity on the bill of materials that hasn’t been consumed through earlier receipts, that quantity will be backflushed when the manufacturing order is closed.