I am using Windows Phone 8.1 Preview since it was released. From day before yesterday my phone is getting hotter (really very hot) and battery draining too faster. Same happened twice yesterday. I got a minor update yesterday afternoon. But heating up happened even after it. (Battery drainage related to location service is not yet fixed).
Issue was with the hardware. I contacted Nokia Care and after one month I got replaced handset. This issue is not related with Windows 8.1 OS.
I was experiencing the same issue, though the last update solved it for me.
You can always try a hard reset: Reset my phone