The Horrible Effect of Parry

[Kevin]

Hunters must realize that if they use pets against a boss, this also contributes to the problem! A parry from a pet attack is the same as from a character. It's not that pets are "illegal" for use, it's that the Hunter must be very aware of their pet's location relative to a raid boss' position.
-Bolty

In many fights this isn't as hard as it might seem either. If the pet ends up not on the side or behind you can just tell it to stay. Shift your position tell it follow send it back in. It does not need to get all the way back to you either since it will beeline to you and beeline back so you can change position pretty fast. The issue is that while you can move and not delay an autoshot if you stop in time you can't fire steady on the move. But when a beast hunter pet can push over 200 DPS you learn how to deal with it. You also want the pet behind the boss anyway to up it's damage to avoid the blocks and parries anyway.

And with a lot of bosses tanked with the warrior having his back to the wall and the boss facing away from the raid anyway it's not too big a deal.

But yes hunters should pay attention to it. Hunters are very micro intensive this is another aspect, though I do wish Blizzard would make the pet a bit smarter on this issue to cut down on some of the micro.