Yep.
Had the same issue myself.
Tried to explain here :
http://larian.com/forums/ubbthreads.php?ubb=showflat&Main=84244&Number=650109#Post650109Although it's true that the post lacks information, although anybody having "normally" played Arx would get that it's a bit messy. I concur.
It won't be changed though.
Shame, I was starting to forgiving the game its flaws.
(Oh and the last fight was pretty much for me two options : the real hard way, and the real easy way, no middle ground, both alternatives were unenjoyable as a last fight... That also does not make for a good ending)