I've encountered a few broken missions in the past couple days.
The mission with the two guys that study Kagote,
one wants you to look for his friend, who is on the other side of some mating kagote,
the guy you're saving asks if you have an idea, you ask him for an idea, then you can say, i'll turn you invisible,
but, when you turn him invisible he doesn't start following you.
When you talk to him he asks if you've dealt with that Kagote yet.
So the only way to beat that mission is to kill the kagote.
~~~~~
There is a mission where you need to talk to a false neravar preaching about the end of the world.
Your choices are to convince him he's not the neravar,
or kill him.
If you kill him the quest doesn't move forward, it keeps pointing to him instead of the quest giver.
~~~~~
Mysterious killings in vivic,
(i remember the name because it's the one i'm stuck on now.)
I'm supposed to ask about rumers in vivec, go to office of the watch, talk to Elam, ask about work, ask about seven victems, ask about witnesses, talk to peopl in the foren quarter, go to underworks, kill dreamer prophet.
But, Elam is missing the witnesses subjects, and I can't talk to anyone about what happend in the foren quarter. The prophet is also not in the underworks, so I can't just kill her and continue the quest.
if someone would give me the prophet's ids,
I could use the consle to move her to me and kill her maybe?

For the mysterious killings,
For the mysterious killings, you should try my Morroblivion-Fixes patch...
Mysterious Killings Spoilers
The patch contains a fix for an bug where the quest is advanced inappropriately if you ask someone other than the Elam about the Seven Victims first. This will prevent you from asking Elam for "Work". This is the dialog line which will activate the prophet. Since the quest is already advanced, my patch won't fix your saved game.Try typing these commands into the console as a workaround:
1. addtopic 1sevenvictims
2. addtopic 1witnesses
3. fbdreamerprophetref.enable
Then follow the quest as you normally would. If that workaround doesn't work, then let me know and we'll figure something else out.
I'll try to look into the other quests to figure out where it breaks, but this may take a few days since I'm juggling several things at the moment. Thanks for reporting all the details for the bugs you've found.