Ghostman's original proposal:
If we end up going for fantasy instead of sci fi, we could make it a world where instead of magnetic poles, compass needles will point toward mystical locations -- stonehenge-esque megalith structures of unknown origin, holy mountains, eternally swirling whirlpools in the world's oceans, places where deities fell to the ground, gates that lead to other dimensions, etc. That could affect cartography, as it might not make as much sense to refer to longitudes and latitudes when defining a geographic location.
My vision of them, which appears to be very different from Ghostman's original vision of them, is that there exist these fissures and anomalies in the world which take various forms and which I've been calling nodes. These nodes represent magical interaction on a geographical and extra-planar level, some of them are magic additive, and some magic reducing depending on their structure and evolutionary stage (some are active like our volcanoes, some like dead volcanoes, the dead ones are collapsing magic). All these nodes and their magic are aspected i.e for water or fire or light or whatever. All the nodes lead to an extra-planar realm (think wormholes), some of which are small in scale, some large, the tunnels are aspected to the magic of their attached node or nodes. Some times these tunnels connect to other distant nodes, allowing great distances to be traversed very quickly as long as one doesn't get lost in the node tunnels and as long as one can deal with the magical ravages contained therein.

Some societies venerate nodes, and build systems around them, some study them and learn what they can. Some societies have made use of these tunnels and explored them for travel, trade and conquest, and have mined them for magical resources. Some have also done exploratory mining within these node tunnels to find exits where none were known. Not all tunnels lead anywhere. Nor do all tunnels with exits lead to other nodes on our planet, some may lead to exits on other planets in the system, or indeed some exit directly into space. Sometimes certain nodes "wander" leading to unreliable knowledge of the exits or entrances. Sometimes nodes may have been secured by some ancestral knowledge so that they are reliable sources of travel or resources.