Make USB hard disk with OS X bootable as startup disk?
Recently I ran into a similar problem. See 
Problem cloning the startup disk of a MacBook Pro running OS X 10.11.6 El Capitan .

Keep an eye on how you cloned your system partition residing on the SSD. I guess your system partition is of type  CoreStorage. If so, the recipe I figured out for cloning the startup disk may be useful to you.