What version and build of Creo?
You should not be able to do an extrude and add material in the assembly mode, only subtract material.
Are you activating a part while working in assembly or are you making this as an assembly feature? Remember that assembly features are cuts or surfaces only. As Creo currently works the concept of adding material in assembly doesn't exist. If the extrude is surfaces then you might need to check if you automatically have surfaces going onto a layer that is blanked.
if your assembly extrude feature is cut then you have to define which components are intersected by the extrude.