BF quest items and monsters are placed randomly on the third levels of the dungeons, so it is possible for any particular dungeon to have none, one or multiple items or boss monsters. All the quests should be solvable within the 3 dungeons for act 1.
Sometimes a dungeon level entrance can be partly or completely obscured by a wall. You already checked the auto map, to see if you could see some blue sticking out somewhere. Running around methodically searching with the mouse can also help.
Occasionally the entrance can be a pile of rocks, rather than the usual fountain thingy.
Rarely part of a level can be separated from the rest, which could contain the entrance to the next level. Can you see any other walls, etc on the auto-map?
In the main game there is a way to get a summoning doll through a wall and then enter and leave the BF to get your characters there (
armory trick in act 1). Since you are in the BF already, that will not help (it could in acts 2 or 3, where you would have teleporter stones and could have a doll drop one on the other side of the wall to get your characters past). It is possible the entrance could be within range of a summoning doll, though.
Alt-tabbing out of the game and back can shift character positions slightly, so if you get both characters as close as you can to a wall you may be able to alt-tab repeatedly to get them through. Doing this with other NPCs around can cause problems if they get through a wall and become inaccessible.
Teleporting anywhere (via hex editor)Alternately, if you haven't done so already, you can just skip the rest of that dungeon. You may miss a couple BF quest solutions, but completing the BF dungeons is not necessary.
