* When Carnival makes it to Hell, she is very well ''alive'' and in her physical form. Up to this point, Menoa has been established to have power over ''souls'', not on actual bodies. So, why is he able to change her shape at will?
* What is the difference between distilling 13 souls to make angelwine and consuming 13 (or more) soul pearls? Jack Caulker consumes an unknown (but huge) amount of soul pearls and then [[spoiler: is killed by Menoa's forces]]. Shouldn't that have been impossible? Also why don't the other soul pearls, which are supposedly worse than the one he took initially, cause him to experience a torrent of visions of their deaths?
* When Dill [[spoiler: has his soul displaced and Silister Trench takes his body, his wings are burned by poison and Rachel is forced to cut them off]]. She doesn't bother to hold on to them though, despite knowing, or at least having no reason not to believe, that once Dill is returned, his angelwine-powered healing will take over and they can be reattached.
* In the end it's revealed that there's no time in Paradise, because Ayen expelled it along with Sabor's castle. Then how could Ayen become an old lady at all, and how/when/why did other people in Paradise die?
* Why did they have to go back to year 0 ''at all'' in order to go through Paradise's doors, if there is no time flow on the other side?
* The main quest in the last part of ''God Of Clocks'' is preventing Menoa from killing himself, in order to stop him from going to Hell and seizing power there; so they go back to year 0 before he can kill himself... and find Menoa standing by Paradise's doors. But ''which'' Menoa is this one? If he's the original Menoa (before suicide), how can he know who they are and what do they want from him? And if he's a future Menoa gone back in time, then ''where'' is the original Menoa?