I encounter the regular “disc not ejected properly” error related to Time Machine since. I am not sure this problem is relative to Mac OS X 10.11 El Capitan only or not. Need to know someone’s experience.
Well this happens on Yosemite, Maverick or any Mac OS X versions guy.
This occurs on the users who tend not to know the way to Safely Remove the External Hard Drivers.
You can attempt to verify and repair the disk by Disk Utility, then make sure you do not loose cables and failing hubs gain.