It has to do with the AI city site evaluation, and they only show up when in debug mode, which is what it's designed for (checking AI decisions in debug mode). World Builder effectively trips debug mode, so that's why you see them there. I'd just ignore it, this was mainly something jdog set up for himself, and for other modmakers to check on the AI's city site evaluation code. By the way a site the AI is itself considering will be the color of the civ, the red circle is more generalize I believe; if I remember correctly the red circle indicates a high value founding location that no civ wants to, or can't settle; you would need to ask jdog though in the BetterAI or Revolutions forum.