Initially I thought the same as the OP, then realised that a number of these Skill Points and POI’s seem to be set in areas where a major DE occurs, so it’s just a case of waiting until the DE event. I guess it’s not a bug, but as designed if this is the case.
I don’t know what happens when the number of players in an area reduces. I guess there will be enough alts and new players to keep the numbers up?