lolinc: Game-breaking bugs resulting from careless, silly scripting errors (usually linked with an NPC).
Also, games choosing to simulate the life of NPCs to the degree that such bugs are possible.
For example, if you look at an older WRPG (I'm thinking the likes of Ultima 5 or earlier), when you leave the area, all state regarding such NPCs is thrown away. Therefore, if you kill somebody important, you can just leave and return and they'll be alive and well. Yes, this may not be realistic, but it results in a simpler game with less of a chance for bugs to crop up. (Note that Ultima 6 changed this.)
Or, if you look at a typical JRPG, NPCs aren't handled in a manner complex enough for such issues to arise. For example, you can't do things like attack arbitrary NPCs, so you can't kill someone important. While the simple handling of NPCs might seem limiting, it also reduces the potential for bugs. (Of course, game-breaking bugs can still occur, particularly if the player somehow manages to get story events to trigger in the wrong order.)
Of course, simple doesn't prevent such bugs. For example, in TES: Arena, where you can't attack permanent NPCs (AFAIK), refusing part of the main quest can make it unwinnable. Thing is, if you decline part of the main quest, you should be able to take on that part of the quest later, but in at least one case, talking to the quest giver will crash the game. (Arena is actually one of the less buggy TES games, mainly because of its simplicity, but it is still quite buggy.)
lolinc: Goofy, fidgity inventory systems. . . especially in games with a heavy crafting component.
Ultima 4 and Final Fantasy 5 got inventory systems done right; no limit to the total number of items you can carry, only a limit of 99 of each item type. As a result, you never have to stop and sort out your inventory.
(The one downside of this system is that, if consumable items exist, you can just enter the dungeon with 99 of them and (probably) not have to worry about running out, destroying any attrition-related challenge the game might have.)