Hunter pet buffs aren't being tracked, but it's not quite that simple. I'm not sure exactly which buffs are affected by the second part of the title, I suspect anything provided by an aura.

What I have seen happen:
Shaman is in group, providing Mastery buff.
Hunter has cat pet out and it uses Roar of Courage providing Mastery.
Shaman aura disappears because it is overridden by Roar of Courage.
Cell's buff tracker now shows Mastery is missing even though it is covered.

The reason I am presenting this as a more complex bug than simply "buffs ids are missing from the buff tracker" is because not every hunter will have every pet to supply every buff, especially at once. It's already a problem with pallies and their two blessings and the problem would get significantly worse.

The solution is to check if hunter buffs are present, but not if they're missing.