In NX7.5 I found a bug (PR 6407356).
When in drafting, when I am doing a drawing of a plate that is part of a sub assembly, it adds another component of the plate to the main assembly. So now I have 2 of the same component in the main assembly. There are attributes to keep it out of the BOM, but in a cross section both components show up. The problem is, during modeling, I can hide the component and do some work. Then if I have to hide the whole sub-assembly to work, and then show the sud-assembly, it un-hides the extra component. Just a pain to keep tracking down the extra components. And they don't always appear in the same position as the original. Components all over the place.
I like the idea of a different layer or empty referance set. I will try that. Thanks to all.