After update, now I'm getting "Disk not ejected properly" every time my Mac sleeps Been running El Capitan since it was officially released. Updated to 10.11.4 a few days ago. I have a WD Elements USB 3.0 drive connected to my Mac mini (directly to the rear ports, not via a hub). Ever since the update to 10.11.4 whenever my Mac goes to sleep and I wake it up again, I get a notification to say the "Disk was not ejected properly".

This has never happened with this drive before, not on Mountain Lion, Mavericks, Yosemite or El Capitan until now.

I have another external caddy also with a full size 3.5" drive in it. This is powered by the mains.

It seems to me that the Mac is now terminating power to the USB 3.0 port prematurely (before the disk has had a chance to unmount properly ?), I do not get the message for my full-size disk that is permanently powered.

Tried adding the disk to the spotlight ignore list but to no avail.

Anyone else notices this issue?
I have the same problem with my LaCie 6TB drive which is used by Time Machine and is USB 3 connected. The problem only started after upgrading to 10.11.4. I don't have the problem with my 10.11.4 MBP using Wi-Fi to backup to my 3TB Time Capsule. I have reported the problem to Apple and await a solution.