Morrowind is somewhat buggy. So yes, I ran into it.
(Actually, I never ran into it untill I ran it on XP... That game ran beauttifully on 98 for me.)
Are you absolutely sure it was a dungeon? What kind of dungeon?
I know of one instance where there was a vital NPC that would attack you on sight if you met him early... But that wasn't in a dungeon, and it was fixed in the earliest patch.
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