I am a little confused by what you're writing... Do you use actual bookmarks to plan the route or just the option to open the map provided by the missions?I am trying to decide if something is an “it’s just you” or “working properly” or do I need to try and navigate the issue tracker.
I am evacuating passengers and have been for a couple of weeks or more, how it worked is I start off at the rescue ship and select the bookmark for a planetary base in trouble and the route guides me there with no issues on the way back the mission target options let’s me set up a route all the way back to the rescue ship. This week the route only seems to plot part way eg in the Galaxy map I get taken to the system but no further in the System map I can plot a route to the body and then have to open the planetary map to plot to the base all the plotting can be triggered using the same bookmark at each level, the mission target works the same but is less hassle as fewer map levels are involved. Is it working like this for anyone else?
A proper bookmark (

If it is just the mission's option to open the map, you'd open the galmap with the system of the station marked and would have to open the system map (if available) to find the planet of the station, zoom in on it and find the station to plot the direct route.