I appear to have a similar issue. I use a couple of USB bus-powered hard drives...
On Friday evening, I upgraded to OS X 10.11 from 10.10.5 - which went very smoothly. Following the upgrade, I inserted on of the USB Hard Drives and do a backup. Following the backup and allowing 2 mins for the activity to stop (as I usually do), I attempted to eject the hard disk - OS X told me that it couldn't eject it and gave me to too options;
- Logout and Back In or
I tried again, it didn't eject it - got the same error. I logged out and logged back in, no different. So I restarted and it ejected first time. Therefore it seems that following the upgrading OS X isn't releasing the hard disk. I have only tried one USB bus-powered drive at the moment.
The drive I used on Friday, had only a single USB cable - the one I will use this evening, has two cables. I have a MacBook Pro 2008 Unibody.
I've just plugged in and done a backup to a mains powered USB hard drive and I have the same issue. I've had a look in Console and I've seen the following is being logged;
The volume "volumename" can't be unmounted because it is in use by: ("<UAProcess: 0x7f87ab5378907>:mds_stores (209)")
Therefore, it doesn't matter whether the hard drive is bus-powered or not... Time to provide Feedback to Apple...