Gap Map

[yomi]

So I got this gap map and its amazing I wanna use it more. I assume greyed out areas were areas I haven't visited for a while but I don't quite know what I need to do to trigger the event that caused me to "be there". As you can see in the screeny below I can't go to a decent amount of places including Alice's house where I already had to have been for a quest. Are these grey dots just indicators that there is something or am I missing something? If so what am I missing and how do I trigger it? I would like to fasttravel as much as this map lets me believe I can.

[Pincher]

You can only fast travel to the red dots. Other dots just indicate an off zone you can enter on the route indicated.