When you reach the surface, Li shoots the damned monkeys for no reason. I'm not sure if pets do, but I assume so since they seem to operate on the same principle. This might not be such a considerable problem if they just vanished or popped in a whirl of glowy stuff or something, but they freaking fall into the water and drown (as per the giant turtle thread). I suppose you could leave that in for those who find it amusing, but it shouldn't happen unintentionally I don't think. My wife adores the game on the whole, but that sort of disturbed her... and even though crazy violent games are my bread and butter, I felt pretty bad about it when it happened too. What was worse was that it happens in one spot every time I go back into the Sun Temple if I'm not paying attention. I've managed to accept the fact that there are lots of animals you have to hunt and kill in the game even if it seems vaguely unpleasant to do so (they all respawn anyway), but for some reason watching monkeys drown is just depressing. I think I'd prefer it if they were just part of the background and couldn't be interacted with, even.
Of course, this is just personal opinion, and I'm sure most people aren't bothered by it. I don't know, for some reason it just rubs me the wrong way.