Thought I'd add my 2¢ worth.
It's apparent, reading through the entire thread, that the eject problem happens in a WIDE variety of systems, connections and scenarios. I've had it happen on a 2008 iMac Snow Leopard and a late-2013 iMac Yosemite & El Capitan. I've tried every connection except Thunderbolt. No hubs.
I'm currently experiencing NO problems. Not sure why, but I'll report here in the interest of compiling information. Again, it was suggested to me by an AppleCare rep that updating my iPod iOS MIGHT have included a behind-the-scenes USB driver update that MIGHT have triggered a return of the eject problem. Since then, I arranged for a replacement of my 4-bay OWC HDD enclosure (via warranty), and have disabled Sleep. (I'll likely never update iOS again until this is resolved; it's just an iPod.)
And the eject issue has not occurred since.
No pressing need for Sleep here; my electric bill remains unchanged. I Shut Down at night anyway (habit). I don't use (or like) Time Machine. If that's the workaround here, that's fine with me. But I'd expect a Mac system to perform efficiently and securely. "It just works", right?
After a couple years of this, I'm convinced, as many others are, that this is an Apple issue. And yeah, it shouldn't be real hard to replicate.
Hope this helps.