I am experiencing this issue on my MSI GS60. It starts happening as soon as I use an Fn Key for the first time while running Ubuntu (I have also tested the issue on Arch and it's even worse there).
Ubuntu seems to think there was a brightness up / down keypress randomly (Fn + Up arrow or Fn + Down arrow) even when I am not touching the laptop's keyboard. When I turn the laptop off it shows as if a key was pressed.
I would not mind not being able to use any Fn Key (even though it'd be preferable if they were enabled) as long as I can stop this brightness issue.