I had just started a game and after taking down my first planet in it, moved my colony ship over and started building my command station. I saw a lone bomber moving towards it and sent some ships after it while I moved on to other things. I then received a "Command Station Destroyed" message and panicked, thinking there had been some cloaked ships involved. Upon moving back to it I saw that there was still a ship (Although he brought a buddy with him that I didn't see) and the command station was still there, nearly halfway built at this point. Attached a screenshot.