why is it getting warm ?

What is the chip on the back side of the Yun (that has about the same footprint as the 32U4) ? and why is it warming up so much ?

The chip is AU6350 USB2.0 HUB-Reader Controller
AU6350's operating Temperature Min 0 C Max 85 C ( from IC tech datasheet).
as long as it is in range, it will be fine. Since it is HUB-Reader, you might disconnect micro SD as well as USB device for testing.

If yun working environment is very hot then heatsink could be help.