I do the Mercurio quest and kill him. He drops the Nod fragment which I pick up the scroll appears I read it, Wilhelm talks about it. But then the game refuses to acknowledge that I have picked it up and the story doesn't move on.
I already run in Administrator mode as I've had similar problems before with save game mess ups. Anyone know how to fix this?

just walk outside u have it

I have another situation. I've killed Mercurio, got the Nod Fragment, left the monastery, seen the cutscene with Anexka, go back to University Haven and...nothing. There's nobody inside to talk to, it's got the save point, the rest, the vault. Nobody/nothing else.

Ecaterina isn't there, neither is Cosmos. Going to try and sell some stuff and screw up the game, otherwise I'm over it. Want my whopping $2.50 back, hahaha

You don't go back to the underground haven. You go up the stairs to the University Main Hall instead.