BeagleBone Black won't power up from USB
Part of the chip on your board is damaged, probably the GPIO pin you were playing with, but not necessarily. Maybe you shorted a pin next to it, or damaged an internal buffer - such issues are almost impossible to diagnose precisely. Here are the options you have:


Get a new board. Preferable if money is not a problem, and you need to trust your BBB. Using a damaged board in your projects will make them harder to debug, since you won't be sure whenever a bug is due to your HW or SW, or to the chip fault.
Try to disable the pin. If you can reprogram the pin you suspect in a state which stops the overheating, you'll substantially prolong your BBB's life. Try to output 0, 1, configure it as input and see if the excessive current draw stops. Then apply that config on each reboot.
Live with it. Since the chip is getting hot, it may not last very long, but you never know.