Setup for module-in-module needs to be planned with care (no rocket science, though; a couple of basics need to be watched out for). Life is easier with nested off, but sometimes you really need to use them. Say you have a unit plan module, and within it a HVAC unit module which repeats across different unit plans, so module-in-module is the only way to go. If the HVAC module master layer is on, all its elements will (obviously) get published in the HVAC module along with the unit plan module, even if you don't see them in the unit module publishing view. I have not done it for a couple of years now, but I remember thinking it through quite seriously. I'd have to check what I did exactly the last time (and I can't check now, but can if needed after Tuesday), but off the top of my head a bulletproof path would be to publish the HVAC modules and place them into the unit creation stories, and then publish the units with nested modules off and all the desired HVAC module element layers visible, so that the HVAC elements will show on the unit plan publishing view (the HVAC mod master layer will obviously be visible in the unit plan publishing view, but with nested-off the HVAC module will not be carried through as a module with the unit plan into the building plan).
Have you checked duplicates? Messed up setups for nested modules immediately result in duplicate elements, their numbers doubling with every update, so it very soon gets crazy.
The other killer is elements from other stories visible. Just say no. And unless some exceptional situation requires otherwise, everything displaying symbolic, own story only.
