When you design/build a custom ship, there is no icon for the map after it's launched, just a leeeetle dot. I you don't pay close attention, you can and will lose track of your ships. It's not bad when you build an extended range colony ship, it just goes to a panet. But an enhanced range transport and attack/defense ships are very, very hard to keep track of.
Minor point, but trying out all the things that I can.
pek