You have to completed Missions 12 to unlock the area that they are in and then complete Mission 14 which is the mission at allows you to ride chocobos. Missions 12 is a red Ce'ith Stone which left of the way that you first enter the main hub map. Go left and follow until you come to another left turn into a valley. You'll find a red barrier and red Ce'ith stone. Complete that and behind are the chocobos and then just completed Mission 14 which I think is back there.