Do you have an alert set for a condition that's normally active, such as Phone Signal, Silent Mode, or Bluetooth On?
If you look at the notifications screen in LF, it will show the color you've set for each alert. Which one(s) are red?
I disabled the notifications for everything and that damn red indicator is still on when my screen is locked. I am unsure of what that is but it is annoying. Light flow seems like a really cool app but it isn't working correctly for me. :-(