I've experienced this problem on my 100x hunter as well, I'll try describing it and once I decide to play arenas I'll even provide screenshots
So what happens is you are allowed to summon your pet in arena, everything is fine, but as soon as your pet takes a hit (doen't die, just takes a hit) his action bar disappears and all the spells become unussable (even if you got them macro'ed). You can see your pet running around, auto-attacking people, but you lose control over it.
The bug is actually 10/10 because you can't use one of your main defensive (roar of sac) as long with stuff like crit buffs etc :p