Gamasutra has an article up called "Neverwinter Nights Client/Server Postmortem: How I Learned To Stop Worrying And Love The Magic Missile", by Mike Brockington and Scott Greig, and based on this year's GDC lecture. Going far beyond mere client/server problems: it discusses various problems that can occur on a very big, very long project with 25 programmers.
The problems with NWN's reputation system, like most bugs that affect creature behaviour, make for hilarious reading:
The orcs were placed in the Aurora Toolset, the module designer then starts the chapter, and plays through the chapter, testing for balance. By the time the designer reaches the area containing the orcs, there is only treasure lying on the ground; the orcs are long gone. The AI was accused of forcing the creatures to drop their treasure and run away. Upon further investigation, the orcs had been told to "wander" near the area that they were standing in. Nearby, there was a large encounter area that spawned deer. However, orcs are hostile to deer. So, the orc would "wander" into the area, and a deer would appear. The orc then proceeds to make short work of the deer. All is fine in the world, but the deer don't like orcs any more. The encounter area resets, and says "there's a hostile creature nearby", and the deer runs headlong at the orc. The orc says "Fine! Deer Stew #2 coming up!". Repeat ad nauseum. Unfortunately, the orc doesn't have an unlimited capacity to heal himself. After about 25 deer are spawned in, they finally get enough lucky attacks on the orc to kill the orc outright. To tie things off, the encounter area would reacquire and destroy the deer, since keeping extra encounter creatures that weren't actively fighting or watched by a PC was just a waste of CPU time. Hence, the orc's treasure would be left on the ground, and no sign of the victorious deer was to be found!