Bonus links must be placed next to or on top of the bonus they correspond to when possible.
All territory connections must be visible on the map. Any time you have objects that connect over long distances, or territories that are split into multiple objects, it must be visually apparent.
Look at the cities on the bottom, and then look at the entrances. The entrances are the same territory, top and bottom.
Suggestions on how to get this fixed?
It is important to note that those hexagons are NOT zoomed out cities, but rather entrances to underground.