Quote Originally Posted by Cilia View Post
Contextually speaking, the problem is that the crystals don't show up until after Emet-Selch has been defeated (or at least we don't find them until then), thus the argument is that he survived and put them there. That can't really happen if he's dead. How then did they get there? Well... see below.
Seems to me the answer is that he put them there beforehand.

Personally I think the most probable culprit is the Hythlodaeus shade put them out, considering it gives you the forbidden Azem soul crystal later on. Which, admittedly, acknowledges it may or may not be acting in accordance with Emet-Selch's will.
Hythlodaeus is just Emet-Selch's construct. Anything you attribute to him is in reality Emet's will by proxy.