Dungeons, huh? From what I remember, well before the first Cataclysm people called the central den of the monster zones as Dungeons. A total of 24 dungeons are present on planet Vermillion, corresponding to the 24 danger zones.
What were the Danger Zones? They were the places where an S grade monster or higher ruled over the other monsters. The more you move to the centre the more dangers you will come across. At the very centre of the danger zone, there exists a central building where the ruler monster sits. The reason they called it a dungeon was because until that time they could only reach the central area of a couple of danger zones, each of which coincidentally had a dungeon each.