Spoilers
If you've done the asylum, change into the slayer, you'll lose two points of rep every time you do.
One quest that will lose you 2 points of rep is the buried alive quest (man in open grave in graveyard). When you go to confront the blackmailers and free the noblewoman tell her you're going to collect on the ransom instead of letting her go. When you go get the ransom you'll lose rep.
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