Here I'm going to list all the hunter pet glitches I've encountered which make the game practically unplayable in certain situations.
Movement speed: Pets' movement speed is based on their owner, not on their own base speed. Their speed takes over once they enter combat, however before this you can easily slow them by using concussive shot or hamstring on its owner. This also means that fast pets such as Takk the Leaper are disappointingly slow, not even able to chase down a mounted player unless you have both the speed talent and Aspect of the Cheetah enabled. Either that, or you have to have him tag a mob once in order to be as fast as he should be.
Line of sight: If something is not within your pet's line of sight, he will refuse to listen to any of your commands related to that target. This is definitely incorrect; the pet should be able to attack anything as long as you have it targeted and there are no obstacles making it impossible for it to reach your target.
Focus abilities: These are not cast automatically unless you have your pet set to Defensive or Aggressive mode. This forces hunters to have a much higher APM than was originally intended. Even worse, some focus abilities, such as Claw, will only autocrat once around every 8 seconds or so, which drastically reduces pet DPS.
Inability to chase: Not directly related to pet movement speed, however sometimes my pet will completely stop chasing people, which combined with the movement speed glitch allows mounted players to easily escape. I noticed this happens especially in Searing Gorge.
DOTs causing Aspect of the Cheetah daze: Makes playing against priests extremely difficult, as they are already my hardest matchup. Trying to keep distance is impossible with this.
If anyone has any other glitches they'd like to share relates to hunters, feel free to post. These glitches have been in the server since its release and it's become very aggravating.