Too much usage from an application or background app can make it overheat. Like for instance if you are on Facebook and playing a live stream it will start to overheat because it has to use more RAM and CPU to get it to keep at a steady pace with the app.
Some apps use too much of your CPU and will make it overheat even if it is a small application. Pokémon Go is one of the reasons why it over heats especially with other apps. Too many background apps, too many apps on your iPhone, too much storage being used, too many notifications.
There's a lot and that's also includes Photos too and FaceTime, calling somebody, there's a lot but just put it on airplane mode so it doesn't get so hot and turn on your wifi. It helps reduce the amount of CPU usage being used.