Funny you should ask, this started happening only the past 2 days and only a handful of times. Turning screen on and off fixes it.
It's not completely unresponsive, it just registers touch really really bad, like only 1 of 5 taps. Seems like a software or firmware problem. I remember having a similar issue with the nexus one digitizer in the early days, where the bottom half of the screen would sometimes misregister input, always happened while charging, when it's almost full too I think. My theory was that some excess current got dissipated near the connection of the digitizer. Because of how it uses electric current to register touch, this would cause it to misregister.
However last time this happened on my N7 it wasn't charging. So the other theory seems likely, the smart case magnet in some way disrupts the capacitive screen.
In any case, turning the screen off will kill the digitizer connection and recalibrate when turned back on.