I am running the current version of the game, on windows 10, no mods, downloaded clean and unzipped into it's own folder, not using any unofficial ports either. The problem with the mouse navigation does not happen all the time nor with all the locations in a system. It is all of the systems though. It usually is something like the station, but once again it is not everyday or every place, meaning every new day there are places that you can't get to with the mouse alone and it can and does change. You are playing the game, then you click a location to travel to and it looks like you are, but you just don't for some reason and you have to use your key board to get there. You can high light it with your mouse and hit enter or move the cursor to dead space and use the arrow keys to highlight where you want to go then hit enter.
Also for whatever reason the mission screen for Quthor does not show up after you get authorization to navigate the system and trading privileges. It does show up a lot later, sometime after you get the map fragment, but that was on the previous public release, 1.50, I have not made it that far on this play through so I am not sure if that still happens.
Below is a link to a save file if it helps.