I bet they got hungry seeing as Jack and Ennis let the dogs guard the sheep while they stayed in camp. Poor things had to wander off from time to time. Heck, we can take the dead sheep Ennis saw as evidence that the boys stayed away too long and the dogs let down their guard.
The attack on the ewe could have occurred because the dogs wandered off, or it could have been an attack of a pack of large coyotes or even a normal sized wolf. The dogs simply could not have alone protected the sheep under those circumstances. In any event, the shame on Ennis's face showed that he understood that he and Jack were responsible, the whining of the dog showed that the dog understood that it had failed in its role as well.
I believe that the dogs had to be fed, no rancher I've talked with in the Northern Rockies has confirmed to me that sheep dogs live off the land during the summer grazing season on public lands.
In today's ranching world, often horse feed is helicoptered into the area. I think that we can all agree that Aguirre had not yet bought his first chopper, so hauling up the feed up the mountain would have been difficult. But, horses are valuable and I think that Aguirre would have fed them before he fed the "two ranch stiffs".