The companions are separated in to groups of 3 for each daily quest hub, i.e. mogu, mantid and yangul. You start with one and additional unlock via arena quest at revered and exalted. If you are missing one, it's probably because there were no dailies for a specific hub in a while.
Currently it's bugged. To get the credit make sure that both you and your companion are dismounted when you turn in the quests. Sometimes you'll need to mount up and lift off, for your companion to fly with you and then land for him to dismount.