What could be the cause of phantom pain?
I would call it muscle pain, or myalgia from using muscles you did not train before.
It is normal that it disappears when you are using the muscles as this kind of pain is one that will 'go away when you do more'.

If it is a light aching, I would just ignore it and go on with your current training schedule.
If it is painfull enough to keep you awake or keep your attention while doing things, slow down on the cycling and do not do as much or take more time in between sessions.