These white dots pulse slowly on my scanner sometimes, on various planets. They will show for about 1 second, then not show for a few. I took the picture underground as at this particular moment there were a lot showing, but they also appear above ground as well.
I have tried to track them, they are usually a long way away. The only time I have been "successful" is when I found a structure of some sort, but I cannot be sure the dots actually mean "structure is here," as other times I have tried to track them and have seen nothing.
I'm starting to think that they are life-forms, but do not have enough data to corroborate.
Also, no, they are definitely NOT waypoints.