Unfortunately, if level 3 of each of the dungeons is clear, then I don't think there is any way to complete the remaining BF quests.
Do you have the 1.47/1.49 patch
installed, or an already updated release / download version? The version number is listed in the bottom right corner of the main menu.
FWIW, I didn't clear any of the dungeons the first time I played through the game, and didn't have any problems levelling.
Did you find the ingredients to make some explosives (you could find a book describing how to make gunpowder)? Using the explosives to exit act 1 gives experience; taking the stairs up near Samuel's lair after defeating the guards there does not.