who or what did Mr Eddy shoot towards the end of the movie?

Same here --- as we all know in fact William Eddy in truth was a hero as far as anyone could be in the historical truth of the Donner Party --- so I doubt he was shooting at a human unless It was Foster --- Tragic story made more confusing by this film ---

Yes this was one of the fair amount of things that was confusing with this movie. I assumed it was an animal that he shot (bad scripting because there would be no animals) as I didn't really notice anyone disappearing from the group. And I don't think some lonely person would wander in that area.

If they actually spotted someone that wasn't from their group they would likely assume it was someone that was part of a rescue party and they wouldn't shoot.

It was a deer. Eddy actually about a deer late in the ordeal.