The transition from Thomas's shop to the Deep Lizard Boneyard is broken.
The transition into the Drow Caravan quest is broken.
In Underdark - East, the transition that once lead to some small camp in the northwest corner is broken.
Possibly a broken transition at the northern side of the base of the Spire. I've never entered this one before, so not sure if it ever went somewhere or if it's one of those blocked off quest entrances.