Update: After looking at this more closely, it appears that the tool tip is whatever station you had highlighted.
So, from 3D view, mouse over a station then open the Nav Map and the tooltip will be for whatever you had highlighted when you opened the map. I'm not sure this is a NewUI bug actually.
Using SH5E if you mouse over the gray border around the Navigation Map you get a tooltip for the hydrophone station. This seems cosmetic only, since clicking apparently does nothing.