After update, now I'm getting "Disk not ejected properly" every time my Mac sleeps
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.