Make sure they have withdrawn their chocobo as a fighting companion. If it is out it won't let them put it in the stables. Maybe check in the FC settings for rank and permissions for the each rank. This must be set for each rank you have for members to stable their chocobo. Go to FC menu/rank, right click the rank and choose hierarchy settings. The message sounds like you don't have that permission active for your friends rank still. Check both stable and training other chocobos. It something small that being over looked. Good luck!