Do you remember if the light was still on in the Air Cleaner? and the little fan running?
If you were standing inside, and none of the modules had the "no power" icon on them, then the Air Cleaner should be able to make enough oxygen to keep you alive and slowly fill the base. But maybe there was a bug where the air cleaner thought it wasn't powered for some reason. Not sure.
See if you can grab a screenshot of it next time if possible? Or if it always happens to you with a particular saved-game, zip it up and email it over to me and I'll gladly take a look (steve@cairn4.com)