For the quest here:
http://www.uesp.net/wiki/Morrowind:The_Scholars_and_the_Mating_Kagouti
I've completed the quest in Morrowind by killing both the Kagouti but for some reason in Morroblivion despite killing both the quest is stopped because it says I haven't killed them even though I have.

I'm working on this. Will provide a fix by the time v056 is released.
Okay, finally finished this: http://www.mediafire.com/download.php?6nma4o4akvg2xrt
Was this bug fix added to v056? This page was sitting below a load of bugs that Thermador labeled as "fixed", but this fix is still labeled "ready to commit" and isn't listed as one of the mods included in v056: http://morroblivion.com/forums/morroblivion/mods/753?page=8#comment-21588
No, it wasn't. That's why it's still 'ready to commit' :)
Merged in v057
I am playing with v060. When I encounter the kagouti, they are not aggresive - they just keep on wandering (Editor package - wander near location). I do not engagem, just walk by to find the other scholar. I see the other scholar, and when talking about Kagouti, he says he was cornered, and talking about Kagouti again (without killing them), he mentions that he is glad I was able to kill them.
This quest bugged out for me - the kagouti were non-aggresive, and the scholar assumed I had killed the kagouti and the quest stage progressed without any such action by me. Thoughts?
EDIT: On further review, the quest plays out fine if I choose the "My Friend" topic from the stranded Dunmer's dialog tree. If I click on "Kagouti" topic, then he assumes I have slayed them already - so this is the minor problem. The quest plays out fine if you select the "My Friend" topic, and he gives you choices on what to do with the kagouti. I chose to slay them, but the kagouti are non-agressive (by design? - as they are much too strong for a new character?)
Hope I am not stepping on any toes here - Just changed status so this will be visible in open items to others.
Yes, kagouti being non-aggressive is a feature - otherwise they'll slaughter the questgiver pretty much instantly.
I'm not sure how you were able to progress the quest without actually kiling them, but I've now put explicit conditions on 'Kagouti' topic from Edras Oril, so this should not happen again.
Changes merged in v061.
Hey, just wanted to let everyone know, I'm playing v061 atm, and just ran across this bug. I used the 'My friend' topic to start the quest, chose the option to kill the Kagouti, go kill them, come back and use the 'Kagouti' topic to try and finish the quest, but he just acts like they are still alive. Not sure what's causing this, but it's still not fixed as of v061.
EDIT: Also, the dead bodies continue making mating noises, even after they are dead. They are definitely dead, I can search them, but they continue making noises and the quest will not continue.
Did you start this quest from Edras Oril?
Try this esp:
That fixed it, working perfectly now, cheers.