Confirmed bug. I placed armory small prefab and hallway small prefab directly above it and sure enough after leaving level test the prefab library was emptied.
This does bring up another "bug" errr... "feature". When adding a prefab the entity and segment library automatically fill with parts used in the prefab. This is uneccesary clutter AND it creates a problem because doors are placed into the entities library and of course doors don't work real well as entities
...well unless you want to make fake ones or you like door shaped wall hangings