I sent Katja back to the Boneyard from the Mariposa Military Base. The problem is, when i come back for her i don't have the option to ask her to join again? It's like I'm talking to her for the first time with the option to follow me excluded.

Am I missing some mechanic here or is this a bug?

Everything connected to the Boneyard is very buggy, so it could be a glitch.
Have you checked your Intelligence and Charisma stats yet, maybe they're decreased.
She usually joins after you tell her you don't plan on staying at the Boneyard.