"Disk Not Ejected Properly" error after EL Capitan goes to sleep and wakes up again.

I'm using a 3 TB D2 Quadra linked directly to my late 2012 iMac with a USB 3.0 cable and this setup has been problem free for three years until El Capitan. Time Machine backups seem to be ok but I also use Super Duper to back up the entire disk on a regular schedule. Lately on wake up there is the "Disk Not Ejected Properly" warning and no back up has taken place. I have tried a number of other "fixes", updating the driver, using Disk First Aid but nothing seems to work. I'm going to try using a Firewire 800 cable and see if that makes any difference. Hopefully this problem will be corrected shortly.

Disk Not Ejected Properly

SMC reset worked to solve it for me (MBP Retina, late 2013) - Resetting the System Management Controller (SMC) on your Mac - Apple Support

Thanks! Resetting SMC worked for my MBP Retina also.

Did not think it was necessary with a brand new (3 day old) MBP. So far, so good.

I spoke prematurely. Resetting SMC worked only in testing and putting the MBP Retina to sleep for a few minutes. When I returned to my office after lunch, I got the same "Disk Not Ejected Properly" message. This never happened before El Capitan, nor on my last two MB Airs, in the past five years.

Same problem here. Have already spent $400.00 recovering a 1TB drive. Called Apple about this and they had me reset VRAM and something else. Did not help. All of this only began after instal of El Capitan. And this was supposed to be the OS X version with few new features but lot of details to fix issues. Som much for that goal.

problem still here after 10.11.1

I've also been having this problem since upgrading to El Capitan with 2 external drives, both connected via USB 3 to my nMP. The external Pegasus R4 RAID connected via Thunderbolt doesn't have the issue. When I wake the computer, even though I have the warnings that these USB drives weren't ejected properly, they are still mounted, so Im not sure if it's causing any issues in of itself, but I didn't see this problem before El Capitan.

The funny thing is, if I manually put the computer to sleep for a few minutes, after waking it, I don't see the issue. It seems to only happen when the computer goes to sleep for an extended period of time, 5 hours last night.

New iMac with El Cap. Same issue after machine sleeps overnight, not for shorter periods during the day.

Before manually putting the computer to sleep last night via the Apple Manu, Under System Preferences/Energy Saver, I disabled (i.e. removed the check mark next to) "Enable Power Nap" and this morning I didn't have the warnings. We'll see if this continues to be a workaround, but I shouldn't have to do that!

Having the same issue. Upgraded to 10.11.1 from 10.10.5 last friday and everytime I wake my Macbook Pro from sleep I get the ejected incorrectly message. Never had this before. It's a Western Digital Elements 2 GB hard drive in 2 partitions, connected to my 24" cinema display. I replaced the cable but this didn't fix it. I got them now connected directly to my macbook to see if it makes any difference. A really weird bug..

I was hopeful for this work-around. But it did not work for me. Same "Disk Not Ejected Properly" message if it's in sleep for more than a few minutes. I was also hopeful that 10.11.1 would fix it. It did not work.

No workarounds have worked so far. The latest OS update did not fix it.

Yep, my work-around has failed me today too. Sorry. It's really odd that when I wake the computer, the drives are mounted. I was looking to see if there was a log somewhere that showed when the drives had become ejected and was remounted. Anyone know of any logs like that?

The issue seems not to occur when I connect the hard drive directly to my Macbook Pro (it was attached on my cinema display). Do you have your drives connected directly or through a hub? I will also try a SMC reset now.

The 2 external USB 3 drives which Im having issues with is indeed connected directly to my 2013 Mac Pro (no hubs) I Don't have any problems with the Thunderbolt Pegasus R4 RAID.