I noticed this about 4 versions ago, and thought it might go away if I updated to the latest build. I am playing a 60 planet snake map. One planet has an AI SuperTerminal on it. When capturing the planet, as soon as the logistical command station is finished building, the game freezes. The only way to clear it is to log out, the task cannot be cleared in Task Manager. I have a before save, and I've pretty much had to leave this planet alone in order to continue playing.
Updated to 4.058 and it still freezes.