I've been having this problem for some time on one of my external USB drives on my 2008 Mac Pro. It died a few weeks ago and I replaced it with another same external enclosure where I can swap drives. The problem continues, so here's what I've done, which while not a fix, points to the problem.
For starters, I'm running 2 identical external enclosures with Seagate drives on 10.8.5 Mountain Lion. They are DataTales with swappable hard drive set-ups. Both being run by a dual channel e-sata card.
Here's what I did:
1. I unplugged the e-data cable and ran the enclosure on FW800, thinking I had a bad channel or cable. Problem still persisted.
2. Swapped e-sata cables from one enclosure to the other. Problem still persisted on same volume, so it's not a bad channel on my 2008 Mac Pro.
3. Swapped hard drives from one enclosure to the other. Problem switched over to the other volume. This indicates that the latest purchased enclosure is involved.
4. Finally, did all the things suggested above, including unchecking "shut-down drives when possible" in energy saver….nothing helped, problem still persist.
Summarization: It's not the hard drives, nor the cables, nor the type of bus I'm running it on, as it's given me the eject warning on USB, FW800 and E-sata. It appears that the OS does not like certain firmware, as one of my DataTales never ejects and the Seagate USB enclosure before it also ejected after sleep mode. When looking at "About This Mac" and checking hardware, the ID is different between the 2 DataTale enclosures. I may take the latest enclosure and go through the firmware update that I did on the other to run 3TB HD's (a dreaded task as it's complicated and must be dome on Windows 7…no Mac FW updater). I think that some FW on certain external enclosures do not play well with something in Apple OS from at least 10.8, 10.9 and the latest Yosemite from what I've read.
Should I find a solution or if the FW updates works, I'll update my post.
Belkin Hi-Speed USB 2.0 FSU237
Quick update:
The hub I am using is Belkin Hi-Speed USB 2.0 FSU237. It's been working great for years. I've had other hubs that haven't withstood the test of time.
I plugged my time machine backup drive which is a Western Digital 1TB USB 2 drive directly into the USB port on the computer (no hub). I got the same error on sleep. It didn't happen every time, but it happened over half the time I tested. I tried several USB cables. The full description that Disk Utilities gives me for this drive is: WD Ext HDD 1021 Media
It seems like I'm going to need to purchase Jettison. Since the problem is occurring even when the drive is plugged in directly, I'm not convinced that purchasing a new USB 3.0 hub would solve the problem. Because I use the drive for manual Time Machine backups it does get written to. Most of the other drives plugged in are used in a more read-only fashion.