If you have ships adjacent to a planet you wish to colonize and you colonize the planet where the colony ship sits on top of another ship just before colonization. The other ship will disappear (but you are able to select them and see them again... but you have to know they are there.)

The screens show how to reproduce.

Set up ships in from of planets to colonize (Vallus in this example) select colony ship and colonize. It will go over the scout vessel. Once you close the planet screen you see this...

But you can still select the ship as if you hover over that spot you get...

Selecting the hex will bring the ship back to view. Although I've only shown this in the close view, the icon is also missing when zoomed completely out.