PSA: If you are having trouble with your pals leaving their breeding pens

... 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)