I started a new world on .5011 and on the strategic map all my rare commodities are supposed to be in dungeons yet I go to the chunk and some have towers there instead. Also how do you enter rare dungeons? I went into the cave system and totally explored the first 2 levels and I didn't find anything but the regular bosses. In my prior world at .500 every rare commodity was in a tower. So it seems there is at least 1 bug maybe 2 or 3.
I also had 1 boss out of the 4-5 not spawn in the commodity tower I explored.