WARNING: This may not be a bug, so much as something in need of fixing.
I tried to configure my controls, but in trying to do so I saved something I now regret. For one of the control options you can change the regular clicking of the L Mouse Key into something completely different. So now even when I exit the game and rejoin to play a session of 'Oxygen Not Included' I'm not able to click on anything... I'm still trying to find out what key I configured the controls to. But it would be much appreciated if this were not to happen again. My suggestion would be to make the option to switch your L Mouse Key non-existent.
P.S. - I'm not able to play 'Oxygen Not Included' at all, without the L Mouse Key... so hopefully you can get on top of this sooner than later.
All you must do is configure the L Mouse or R Mouse Key to something different, and save the configuration.