In this quest:
http://www.uesp.net/wiki/Morrowind:Gateway_Ghost
1) There're two ghosts flying around the bedchamber, one called simply Ancestor Ghost, one stronger, called the Gateway Haunt.
2) The people in South Wing of the inn attack the ghosts - or maybe it's the ghosts that attack them, I dunno, anyway when you go to the South Wing after starting the quests, fighting immediately starts. That can be fixed by giving people in the inn who have a package to go or to stay in the South Wing a condition not to go there until the quest is finished.

1. This was fixed in v063.
1. This was fixed in v063. Are you using the latest version of the master?
2. Which NPCs exactly?