… check that the breeding ranch is fully within your base’s blue circle.
The building is massive, and the game lets you have part of it outside, but I ran into a ton of bugs with pals going into a weird state where they can’t be assigned after they un-assign themselves to the pen (usually when fast travelling).
(Edit: this is before patch 1.3.0)
My experience was that when i took the pals that were bugging out into my rooster and stepped across the boundary line with them I was then able to assign them without issues. No matter how much of the ranch crossed the boundary.