This was such such helpful feedback, thank you! I think I found the issue and managed to upload a bugfix just before the 24h gamebreaking bug window closed. There were two things:
1. when the dialogue was showing "OBJECTIVE: xyz" it was throwing away all mouse clicks in order to not cycle the objective off the screen. This meant if you had that on screen while losing the mouse focus the mouse just can't come back.
2. Using the options close button instead of escape destroyed the options menu instead of hiding it, and didn't toggle the pause state back to unpaused. In this state the game thought it was paused but wasn't, so you couldn't do anything.
I hope one of those two things sounds like your scenario. Thanks so much for the heads up and I'm sorry it broke on you!!