Not sure if this is a bug, or an intended "meditate while keeping the mouse button pressed" minigame, but it is really annoying - i even managed to fall asleep once while "playing" it, just to find myself somewhere outside of the visible system map (btw: is the hyperspace ruller with it's distances in light years supposed to appear on the in-system map?). If this is related to the new autopilot you may consider making "set waypoint" a selectable option (or even a "set waypoints" - path setting will be usable to go around various nav hazards).
Not directly related, but making "Lay in course" non-default option that has to be specifically chosen in the object popup menu was really bad choice, as in most cases that is exactly what one wants to do when clicking on object (at least you did put "set as destination" in the planetary menu where one usually ends instead). "Go to the system" may be arguably better on the hyperspace map, to allow one to set in-system destinations, but you really have to make "Lay in course" default for system maps with the next release.