I may have figured it out a little bit. Its a bug in Waze not in CarPlay (although Carplay may expose it).... If you disconnect your phone from carplay while its showing the small colored circles instead of the icons you can see it doesit on the phone as well. It appears that Waze is confused about the zoom level (its shows the icons like that when its zoomed waaaaay out).
What I did was manually recenter the app when the phone is connected to car play and it seems to draw the icons correctly. Not sure if this will work everytime I just fiddled with the app at lunch to see if I could make it work.