I heard this story through oral tradition (an artist friend and Jodorowsky expert related the tale to me.) Essentially, the story goes, no one wanted to slaughter all of the lambs necessary for the procession scene in The Holy Mountain and so Jodorowsky took it upon himself in service of his vision (aka "getting the shot") breaking the necks of the multitude of lambs required.
There is this trivia on IMDB where it's written that
The crucified animal carcasses were borrowed from a local restaurant, which were then served to customers upon being returned.
I don't know the truth and I can't find the source of this but I think it could be interesting.