As suggested in this thread http://forums.autodesk.com/t5/Inventor-General/Red-up-arrow-in-model-browers/td-p/3592634 there shold be a different color other then RED for the extrude arrow. Whether there is a different color for extruded geometry or an extruded cut, doesn't matter to me, but RED means caution/warning or that there is an issue. Black would be fine with me.