The other night, I was playing around a bit as humans. I had recently deleted all my custom ships so that I didn't have so much clutter, and was therefore designing new ones as the game went along.
First, I designed a colony ship. I started with the transport base hull that looks pretty much just like the front command center of the other base hull. I then extended it to about four times it's length with various parts, creating something reminiscent of 2001: A Space Oddessey. Saved it, built one, no problem.
Next, I researched ion drives, and upgraded my design. Opened the shipyard, selected my previous ship, and hit edit. I deleted the old engines, drug the view to the back of the model with my mouse, and added the new engines. I changed the name slightly, and hit save. Then I noticed the icon was not right -- only about half the ship was shown in the icon!
So next time I upgraded it, I made sure the ship was roughly centered in the view when I hit save, and it displayed normally.
However, my scout ship didn't -- it was completley blank!
So the icon generation is a bit off. This is in 1.11; I had never seen this problem previously.