The idea is that a shepherd is out in the wilds, and makes his pie out of the available meat - mutton or lamb, and a farmer has access to his cattle, so he can make his cottage pie with beef.
I was always told that shepherds pie is minced beef or lamb topped with mash.Cottage pie is the same but finished off with a pastry top thus making the "roof" of the cottage. I could be wrong of course but its a nice idea I think.