I'll be brief. This bug was easily reproducible on my end. Simply set a ship up like normal, but in the process of adjusting the schedule, remove all routes from the list completely while having the ship in automatic mode.
In normal 'trains', this results in the locomotive spitting out a red warning repeatedly. I believe it was 'no route' or 'no path'. In Cargo ships, it kicks out a dialogue box and then closes the game out to the main menu. If you need me to forcefully reproduce it for more data, let me know.
Current workaround is simple: Put your ships in MANUAL before you wipe any schedules.