I have been monitoring the El Capitan USB 3.0 problems for a while now. It seems to have started with version 10.11.3. It mostly centers around USB 3.0 Hubs, not everyone is having the issue for whatever reason.
People using a USB 3.0 hub connected to their Macs are the ones having the issues. It seems the hub just stops working in some cases. In others the speed of the 3.0 USB hub is throttled back to 480 mpbs which is USB 2.0 speed. The rated theoretical speed of USB 3.0 is 5 Gbit/s which is 10 times faster than USB 2.0.
I have a friend doing Mac Tech Support at a large corporation near where I live. They have a section that works exclusively with video output using Macs and USB 3.0 hubs. They are having all kinds of problems and will probably go back to USB 2.0 hubs for now.
I don’t think it is the hubs either. I have read articles where people have taken those same USB 3.0 hubs and attached them to other Macs with other OS’s and they work just fine.
As for me I have had no problems with my Sabrent USB 3.0 hub. I only bought it three months ago, so maybe that is why. It is a 10 port hub:
I have all kinds of stuff (several hard drives) attached to it and have had no problems with it so far, I am currently running OS X 10.11.5, the most current OS. So, what is the solution?
Some people are just trying other USB 3.0 hubs. Others are going back to USB 2.0 hubs as previously mentioned.
Some people say “zapping the PRAM” fixes the issue, at least until another El Capitan update comes out. On modern Macs this is called resetting the NVRAM, same thing. You “zap the PRAM” (resetting parameter RAM) by restarting your Mac, as soon as you hear the startup chime you hold down the Command Key ⌘, Option Key ⌥, “R” Key and “P” Key (Command-Option-R-P) all at one time until you hear the Mac restart chime again. Then let go of the keys and let the Mac bootup normally.
What this does is to force the Mac to go out and reconnect with all external hardware which somehow gives the hub a fresh start.
At this point there is no fast and true fix for this issue. If you are having this problem you can try some of the above solutions, perhaps they will help. The bottomline is that Apple is really the only one that can fix this in El Capitan. Just have to wait and see what happens.