I've been using a MacBookPro, early 2011 with an external drive for a number of years. I've never seen that message unless the power went out or I inadvertently unplugged the drive.
I now have a late 2015 iMac. I recently purchased an Insignia USB 3.0 hub and an external SSD. Both the SSD and my old USB 2.0 drive plugged into that hub. Now when I wake the computer in the morning I would have at least 10 of those notifications. Called Apple and they didn't really know, so they had me try various fixes, with no luck.
I bought a new 4 Terabyte USB 3.0 drive and plugged it directly into the iMac. So far, no notifications. I still have the hub with keyboard, tablet, iPhone all plugged in. The SSD I plugged into the router.
I think my issue may have been related to the hub. Sure, I could have taken a chance and just replaced the hub, but I really wanted better performance from the external drive.
I don't think it OS related.
I hope that helps someone.
Good luck!