for the first, you may consider not putting shoes on top of each other because the shoes on the bottom will get dirty.
as to the second situation, do you mean passing infront someone? I think it can be rude if done in a certain way, i.e. the person is standing too close. it is like cutting someone off on the road.
Is there anything wrong with putting shoes ontop of shoes or is that cultural? And is there anything wrong with stepping over someone to get thru or is that cultural too? My mom never let us do that , we had to go back and around.