I started a new game with a custom faction and found 2 bugs. The first is that when I upgrade ships I have a long list of the same ship, in this case a scout, over and over dozens of the same ship. This appeared the first time I upgraded a ship and has persisted every time I upgrade I have to search through dozens of the base ship to find the upgraded version.
The second issue I found was requesting constructors, I already had a colony ship queued and requested a constructor. When the colony ship finished it automatically moved to the starbase requesting the constructor.