Well for one, the fact that they don't nest properly. They mention that you can get the address of the parent hexagon by truncating that of the current one. The problem is that doesn't actually work all the way up because certain tiles on the border will flip back and forth in strange ways. They had to do something to deal with this, just like the would have had to do something else with squares having two kinds ot neighbors. The squares issues are more obvious though and the code to deal with it will probably be very localized.

I mean, don't make a nested spatial index with spacial regions that don't actually nest. The structure fails at its primary claim.