You might want to check the temperature of your phone when this happens. Touch the phone to feel whether there's any abnormal heat. Waze is a battery intensive application because it uses the GPS, radio, screen, and GPU, it is normal that the phone would warm up a little when running resource intensive apps but it should not be too hot to the touch.
You would also want to put the phone away from the car's heater on winter, and shade it from direct sun light and turn on the air conditioner when it's summer.
It's probably not the car charger, but not charging while using Waze may also help a little because charging causes the battery to warm up. This may not be practical though, since Waze uses lots of battery while running.
If there is an option in Waze to turn the screen off on long roads, then use that, the screen is also a major producer of heat.