There seem to be two "Nine Miles:"

1) Nine Mile (or Ninemile) is a spot approx. 25 miles west of Missoula where Nine Mile Creek dumps into the Clark Fork River. The creek crosses under old Highway 10 and the old MILW right-of-way (I think the rr bridge has been removed). Access from I-90 Exit 82; Nine Mile House is (or at least used to be) a decient restaurant.

2) MapQuest also shows one in southern Butte, near the intersection of Harrison and Continental .... don't know if that was a Milwaukee Road spot or not.