Recall that civilian shipping only plans one run ahead. They do not consider the consequences of filling a contract dropping goods off at an empty world. Civilian shipping only uses simple pathing, from wherever they happen to be to the closest available trade run, either public or private. Also, civilian shipping only makes a maximum of one trade run per major time increment. As in, if you run a 30-day time increment, all civilian shipping will only make a single trade run, at most. Conversely, if you cycle 30 1-day increments, all civilian ships may make up to 30 trades runs.
In my experience, civilian ships are awarded contracts in the order they are listed on the Shipping Lines screen, found with the hotkey of "Ctrl + L". Once all ships are busy, they will not accept new contracts until they are finished with their present business. This is why, if you want civilian shipping to handle most of your material transfer, you need inhabited colonies in as many separate systems as possible, particularly along the path you wish installations and other items to flow. Additionally, you want to make use of small time increments and the Auto-Turns feature. Just make sure to have a book with you, or have something else to do while turns process. Whenever you get tired of watching turns cycle, just click the checkbox for the Auto-Turns option again, and after your next time increment, the game will hold, awaiting instruction from you, the Glorious Leader.