Could you upload any pictures? The model, your feature tree etc....
Also there are options to pick from when doing a cut extrude feature in an assembly, you can choose which parts you want cut and you can also propagate the cut back into the part files if you want.
John, thank you for your interest! Sorry, I can't upload that model or pictures, they're third party things.
Have hit this problem twice - on both cases the culprit assembly was an Import, containing a number Solid Bodies. And they were the very entities the openings were needed.
Yes, I'm aware about the Feature Scope option. But, in those cases - and in every case, of course - you can't set the lower level scope to inc/exc upper level assemblies or their parts. This is - and definitely must be - impossible. Regardless, it happens.
I tried to make a some simply assemblies of some existing own right parts I had, but I wasn't able to reproduce the problem. The mentioned imports were not involved in these trials. And as they are third party intellectual property, cannot submit.
Again, I'm about to suspect the display driver. WYSINTT, "What You See Is Not The Truth". Drawing or doc.properties do not show missing bodies or loss of mass. The latter should be present if any real cutting took place.