I've had this problem as well when i had sets built. Contrary to Jeff's suggestion, I found that I had to CHECK the set lists with built sets, because it seems they are added to the needed parts no matter what. Hence, having those.sets unchecked results in needing more parts than the MOC/Set you wanna build requires. Having them checked seems to result in the subtraction of its parts, and thus result in the correct number of missing parts. I agree with the duke, this is a bug.