It happened once when I went into one of the buildings in Mithalas, it showed me as off to the side in black space (with no rooms), I closed it and reopened it and it was fine.
I think it's just a case of the map not knowing where the heck you are since it's a 'hidden' location. It really should show you in the room where the whale is, except you're inside the whale which to the game is another map section, so it confuses the game.