Yes you should be concerned. The batteries in these phones react badly to heat. When you are navigating and charging at the same time the phone is using alot of battery. Its not a one time thing but if it keeps getting hot it can reduce the battery life. I use Navigon all the time I have my car mount set up so my phone is sitting in front of the AC vent in my truck so I can keep air blowing on it.
Prolonged use of Navigon may be heating up the phone due to the constant interaction between the software, GPU, data connection and CPU, also if you're using it on a car dashboard and it's a hot day, this may also play a part.