Jsapp,
Is that enter batch labor?  (my WO-P is different).  If it is batch labor, could it be fractions that are creating problems or outside services?  Our outside services are usually in pounds and the quantity on the work order is in pieces.  When the conversion happens, sometimes it can be a piece or two off.  
 
If it is a major issue, for items on the labor end, you could always go into WO-F (enter labor) and correct the quantity.  As a rule, we correct labor at the end of the run and adjust all quantities to the actual so pieces/hour reports come out accurate.  Instead of trying to distribute it to this or that person, we just use a dummy employee number, no hours, and adjust quantity up or down.

Assuming you are referring to backflushing of components, you need to look at the next level to rule out human error (which is what I suspect).  For the sake of simplicity, let's assume all BOM Quantity per are 1 so to make 1 assembly it takes 1 component.  If you ended up with a negative on hand of subassembly A then for Work order that makes the subassembly, you entered fewer into stock than were consumed by the work order for the next higher level assembly.  Those are 2 completely separate transactions so the user may well have entered different quantities.  To identify a program problem, go to WO-A for the higher level assembly and look at the Quantity complete on the first screen (number of end assemblies made) with the quantity issued on the Component screen you can see when pressing the Materials Button.  If those do not match, then there is a program problem.

What is the Stage 2 quantity of Completed parts?  That is what controls the issuing of Stage 1 parts as components to Stage 2.