HI,
I created a random map, 1 sun. The occupatino planet and sun where a bit too close to my own solar system and when trying to zoom in to see the ships, the lower edge of my solar system well where under the other solar system grpahics, the ship where invisble, etc.
You can see the travel lines when assigning a destination but the ship are invisible until you zooom in very close and the ships would appear (going under the solar system graphic effect I would guess)