Sometimes when you make something there is raw material that is used up, but is wasted so the number of items made is not what you thought. In QB you design a BOM that is cut and dried, you tell QB to build 5 and it does, but if in the actual building process you actually got 4, there is a problem.
You need to bring up inventory adjust, set the adjusting account to the spoilage COGS account, and mark it as a value adjustment. Write down the present value of the 5 assemblies, then change the count to 4, and enter the old value that you wrote down as the new total value. Then QB will recalculate the cost of the 4 assemblies you actually made. The items in the build that were taken out of inventory will not be effected – they are already used up.

