I suspect that this happens because you loose the serial port on the PC when the 32U4 goes to sleep.
When this happens the file handle that the serial monitor uses is gone but the serial monitor does not realise this. I have similar symptoms with a Leonardo and RealTerm when I disconnect.
Only solution to my knowledge is to close and open serial monitor which destroys the old handle because the serial port is closed and creates a new one when the serial port is opened again.