Turns out this was a function of my Varmilo M108 keyboard. The Windows key was disabled, which you can do by pressing fn + Windows key. You re-enable it by pressing the same keys again.
I'd bet it was my cat walking across the keyboard that did it when I wasn't in the room.
The Windows key doubles as the CMD key on mac.
Hmmm this is unusual. It might be something to do with the retina. Oh wait it's really simple: Go to
System Preferences -> Displays -> (Built-in Retina Display) Color tab
In Calibration, drag the white point slider to the far right (most blue light). This causes the screen to become extremely blue, so to cancel this out: