In Act II, I've completed Shar's Temple (stopping short of the point where the player receives a warning about continuing), explored just about everything outside of Moonrise Tower, and finally proceeded into Moonrise Tower, where I slaughtered multiple groups of enemies and shifted a lever to free a few gnomish and tiefling prisoners, who promptly ran out of the dungeon, only for strange messages to appear in my journal about a boat that no-one mentioned in dialogue and that I should secure the safety of those fleeing, but when I followed them outside I received further messages that they had all perished.
I can restore a recent save, but I suppose I need to determine the proper order for doing things in Moonrise Tower so the game doesn't bug out like that.