The disk was not ejected properly

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Your Mac's Specs
MacMini Late 2014, OS 11.2.3, 2.6GB i5, 16GB ram, 1TB HDD
This is a fairly recent development. When returning from Sleep I get a popup:
The disk was not ejected properly. If possible always eject a disk before unplugging it or turning it off. At this point one or two external drives fail to show up in the Finder or Disk Utility.

The disk (WD MyPassport for Mac 1TB USB) is still plugged in. It started in Lion only, but now it's happening in Snow Leopard too. Snow Leopard also couldn't find my Toshiba 1TB USB. It hasn't happened yet in Leopard which is installed on a Seagate 500GB USB.

Using Onyx, I have run all of the Verify and most of the Cleaning options. Reset NVRAM, and did a Safe Boot. Didn't help. The only recent updates are Flash and most of the Mac Software Updates (did not update Remote Desktop or Migration Assistant) I'm beginning to suspect hardware.
 

chscag

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2017 27" iMac, 10.5" iPad Pro, iPhone 8, iPhone 11, iPhone 12 Mini, Numerous iPods, Monterey
You're going to get that error from some external hard drives when left attached and your Mac goes in and out of sleep mode. The problem occurs because the external stays awake when your Mac goes to sleep. Your Mac can put the internal drive to sleep when it sleeps but not all external drives will respond. The solution is to eject the drive before putting your Mac into sleep mode.

At this point one or two external drives fail to show up in the Finder or Disk Utility.

That can be caused by a defective USB bus. Do the drives show up if you reboot? Also, try resetting the SMC.
 

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