If you prospect in some areas, you can find a mine entrance. These mines, if unique to an area, count as rooms that you can visit. The mines are of random size so you may have to find the same mine a few times before you are able to 'visit' all the rooms. My theory is that this is a big reason why in some areas you cannot get to 100% visited without it. Pretty lame, but the only way to find out if there is a unique mine is to find it. Let's keep a list going in this thread.
Aztec Gold Mine --> Prospect around the heart of the one world. You will find an entrance.