I realize this is not helpful, but I too have had problems making bootable clones of El Capitan since OS X 10.11 beta 1 using either Carbon Copy Cloner or SuperDuper. I have no clue why that may be happening. Since Time Machine started working again with OS X 10.11.2 beta 3 I haven't bothered to follow it up any further.
If we knew what it was we were doing, it wouldn't be called research, would it?
