I used to see this happening when I would use Alt-Tab to switch tasks. There are a few other issues this seems to trigger, as well. Since I stopped doing that, I haven't had any problems.
Actually, someone suggested going to the Control Room view, leave the game running at 1x time compression, and then Alt-Tab. The game will pause, and you can come back to it, without the crew on deck and other issues. Seems to work for me.
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