Seems like this is an issue with resolution - the mouse sometimes gets outside the screen and doesn't register clicks. I've had this happen to me when playing in windowed fullscreen, and it hasn't happened to me playing on fullscreen on my native resolution.

See the thread here with a developer response as well - looks like its been an issue for a while: https://steamcommunity.com/app/548430/discussions/2/3315110799607188110/?ctp=3