If you use non-uniform scale outside of sub-object mode, it's going to distort the local transform space of the whole model. If you need to scale stuff, best to do it on the sub-object level: Vertex, Edge, Polygon, Element, etc.
That is what was confusing me, I know that when an object has its scale changed outside of sub-object mode many operations will not work properly. However in my examples I did not scale them, I just created a primitive, converted it to editable poly without making any changes to it and then extruded a few faces and added…