Have had this as well, especially with aurum vale. Mostly though it has been a "bot" instance. These can be recognised as they only have two players and all the trash is still up even though bosses have been killed, as they teleport from one boss to another. Also if you enter a bot instance with nobody in, it will also say 0/3 because they have finished just killing trash for gil/powerlevelling accounts, and left the instance leaving all bosses up.