Atlas Map Issues

My atlas map feels like an rat maze with many routs leading to maps that either wont spawn portals or simply have no way of being accessed. Some of my maps nodes wont spawn portals seemingly regardless of which waystone I put in them. I also keep finding gray map nodes that are surrounded by completed maps. There's a tower thats been cleansed and I seemingly have no way to access.

My entire map feels as though it generated wrong.