It's also inconsistent. As mentioned above, I had to perform a 'do-over' of the fight in the Tadpoling Center. This time none of the javelins or spears lying on the ground were marked red, and Karlach was able to pick up all of her missiles without any problems from the guards. To be clear, this is only a theory, but I think since the Baldurian guards were disgorged from their pods unarmed, they might have picked up some of the loose ammo on the ground and thrown them at the flayers. This then caused 'ownership' of the spears to transfer away from Karlach to the Flaming Fist. Maybe?