I'm seeing a bug pop up now and again where I'll get a new ship, go to upgrade it wiht the latest techs I've researched that are better than the base design, and I'll see a few squares at the top that are blank.  When I go to remove the blank squares it'll remove a component off the model.  These components always have an associated square at the top too, so for instance if I removed a blank that took a troop pod off the model, there will also be a square at the top that is a troop pod.  Removing the troop pod square will take the component space off the available space line.
That isn't that bad, but when I go to the tab that whatever component in question was on, it'll crash to desktop.  That's annoying.  This isn't consistent.  I can reload and go through the same procedure and not get the blank squares.  Anyone else seeing this?