Same here with my 2012 Mac Pro. Happened as soon as I upgraded to El Cap. Never an issue before this. Searched high and low on the web, but no answers. It's not the SMC and it's not a frayed cable. It was the upgrade.
I'm being the follower with "This happens to my computer, too." I can't unplug the device using too much power, because I haven't plugged anything in. This started happening after the "El Capitan" upgrade.
FWIW, the right-side USB port on my "Retina 15-inch, Early 2013" stopped working before the upgrade, and still doesn't work. I tried the two reset steps, didn't help.