I was using 9.3 b1 in my VW CarPlay and it was working great.. Had dinner, plugged back into my car and the it would never connect. I tried a different cable, no luck. I turned my vehical on/off as well as the infotainment system. Also, rebooted my iPhone 6S. Finally I "cold booted" (force reboot) of my iPhone and then it was able to connect. I will update this thread if it happens again. Apple, would you like me to file a bug report?
In other news, I LOVE the AppleMusic updates for CarPlay. Very nice.