"Disk Not Ejected Properly" error after El Capitan

I'm using a similar setup, a LaCie 3TB D2 Quadra connected with a 3.0 USB directly to a late 2012 iMac which for the previous three years had been problem free. Time Macine backups are taking place but I also use Super Duper to back up the entire hard drive. Since the upgrade to El Capitan none of the scheduled back ups have taken place and on wake up there is the "Disk Not Ejected Properly" warning. I have tried updating the driver from the LaCie website, used Disk First Aid and any number of other so called fixes but nothing seems to work. I'm thinking of trying a Firewire 800 cable and see if that helps.

Are you powering the USB drive with a dedicated power supply at all? If not then give this a try. In addition, try using a different USB port, or if you have it use a different USB cable.

I appear to have a similar issue. I use a couple of USB bus-powered hard drives...

On Friday evening, I upgraded to OS X 10.11 from 10.10.5 - which went very smoothly. Following the upgrade, I inserted on of the USB Hard Drives and do a backup. Following the backup and allowing 2 mins for the activity to stop (as I usually do), I attempted to eject the hard disk - OS X told me that it couldn't eject it and gave me to too options;

1. Logout and Back In or
2. Restart

I tried again, it didn't eject it - got the same error. I logged out and logged back in, no different. So I restarted and it ejected first time. Therefore it seems that following the upgrading OS X isn't releasing the hard disk. I have only tried one USB bus-powered drive at the moment.

The drive I used on Friday, had only a single USB cable - the one I will use this evening, has two cables. I have a MacBook Pro 2008 Unibody.

The LaCie is cabled directly to the computer with a USB 3.0, I'll switch the ports around, eject the disks and give it the four finger salute on restart.

I appear to have a similar issue. I use a couple of USB bus-powered hard drives...

On Friday evening, I upgraded to OS X 10.11 from 10.10.5 - which went very smoothly. Following the upgrade, I inserted on of the USB Hard Drives and do a backup. Following the backup and allowing 2 mins for the activity to stop (as I usually do), I attempted to eject the hard disk - OS X told me that it couldn't eject it and gave me to too options;

1. Logout and Back In or
2. Restart

I tried again, it didn't eject it - got the same error. I logged out and logged back in, no different. So I restarted and it ejected first time. Therefore it seems that following the upgrading OS X isn't releasing the hard disk. I have only tried one USB bus-powered drive at the moment.

The drive I used on Friday, had only a single USB cable - the one I will use this evening, has two cables. I have a MacBook Pro 2008 Unibody.

Update....

I've just plugged in and done a backup to a mains powered USB hard drive and I have the same issue. I've had a look in Console and I've seen the following is being logged;

UnmountAssistantAgent

The volume "volumename" can't be unmounted because it is in use by: ("<UAProcess: 0x7f87ab5378907>:mds_stores (209)")

Therefore, it doesn't matter whether the hard drive is bus-powered or not... Time to provide Feedback to Apple...

I have reported this to Apple and asked for a resolution for this...

Same, and a number of times via feedback throughout the El Capitan betas. I hope they address this soon! 😠

Had the same problem with Seagate 1TB external portable dive. USB 3.0. Kept ejecting on me and finally killed my drive. Had to spend $399.00 for data recovery that got all that was on my drive. Called Apple and they have be clear the VRAM I believe it was. All seems to be well now but I thought El Captian was supposed to be the OS X update to fix all issues. What a disappointment. Not to mention rather hefty expense. Disappointed to say the least.

just adding another voice to your note in hopes apple will do something. i also get lots of "disk not properly ejected" notices after i put the computer to sleep. it only started happening after upgrading to el capitan. i have a iMac (27-inch, Mid 2011) 2.7 GHz Intel Core i5. does not affect operation of the computer; just annoying!

I have the problem too: Every morning since the upgrade to El Capitan I see multiple warnings that all partitions on my external disk are 'not ejected properly'. It happens only during the night, not while my MBA sleeps during day time. I presume the disk is ejected at midnight or so. It looks like power is suspended. Can I find out at what time it happened?

You can have a look in Console for 'unmount' events for when the disks are being successfully unmounted. However, I'm not too sure what you mean.

Looking at the areas that are addressed by the future OS X 10.11.2 update - it does potentially look like these USB issues could be resolved? We'll have to wait and see what happens.

The not properly ejected problem persists after the latest update for external hard drive via USB connection. It is happening even when the computer does not go to sleep, sometimes after moments. Very frustrating. For me this is a problem unique to El Capitan. The "Mountain" program suggested in other posts has been of no help either.

I have given my external drive its own power supply. Did not solve... Now I also see that it happens in daytime. Even several times during a long sleep period! So contact is lost and regained and lost again... And worse, it also happens on my OS X El Capitan 10.11.2 beta 2, which runs off that external hard disk: OS X crashes and restarts! So, sorry I think it will not be solved on the coming update...

Apple Support determined that my drive was bad (because it got the same error on a two different Macbook)! Not giving up hope, I bootcamp into Windows and viola! Windows sees the drive and I was able to copy the files. Don't have enough space though, had to order a drive but at this point I think it is save to assume that the old drive will work again after a reformat. I got this error after upgrading El Capitan as well. Windows just become my lifesaver.