Add me to the list of those suffering from this issue, although it has gone from sporadic to EVERY time my computer sleeps for awhile since changing out my USB Hub.
I am running 10.11.5 on a mid-2015 MacBook Pro. I was using a Belkin 4-port Travel USB Hub. It was fairly inexpensive and non-powered. After upgrading to El Capitan, I did sporadically see this issue and while annoying, it wasn't constant, so I didn't worry too much about it.
Now, I have changed to an AmazonBasics 4-Port USB 3.0 Powered Hub and it happens EVERY. SINGLE. TIME my computer sleeps for an extended period (a few hours?). There are literally error messages down the entire right side of my screen when I wake it up.
That being said, my external hard drive (WD 1TB MyBook) is still connected and works with no issues. However, it does not seem to be backing up in the middle of the night anymore and starts backing up when I wake it up in the morning.
I read through this entire thread yesterday, hoping for a solution, and have tried a couple things (to no avail). I wanted to start small, because I'm no computer expert.
I started with switching my browser to Chrome, because I have had nothing but issues with Safari since upgrading anyway. It freezes on me all the time and I have been force quitting it for months. I thought it was worth a shot. I changed the default browser to Chrome, shut down all programs and restarted the machine. Left for the afternoon and when I came home, no joy! Error messages galore! 😟
So I then tried unchecking the Enable Power Nap box. This morning, still no joy. And now I was just away from the computer for a short couple hours and the entire right side of the screen was still laden with error messages upon wake.
And finally, I will note that it looks like my computer does not seem to recognize the Amazon Hub as 3.0; it thinks it's a 2.0 Hub? I have no idea if it's not compatible, defective or what, but it sure looks like the 4 devices I have plugged into it are plugged into a 2.0 Hub (unless I'm just reading that wrong, because it does also say 3.0 Hub in there, but the menu under the 2.0 Hub is collapsible and contains the items that are actually plugged in):

Sorry I don't have anything to add to the conversation, but I wanted to chime in and say that I, too, am having this issue and it's extremely frustrating. 😟