I have a Harmony One remote and notice this all the time. I will have the ATV and change a channel on the cable box or something and the light will flicker on the ATV. I assume it is picking up IR signals from other devices.
The light coming on occasionally is probably the same thing mac computers do to register themselves with the sleep proxy. This is necessary so for instance your ATV would show up on your iPad when you wanted to Airplay something. It would wake up the ATV and start playing. My mac mini does this every 2 hours like clockwork.