It seems that Apple and Microsoft can't get their USB and Thunderbolt drivers to work right. I had a whole slew of error -36 problems when 10.12 first came out. After the second update, it seemed to stabalize. Under Windows, I can't use two of the exact same USB drives on the same computer (it loads, then ejects the devices, rotating betwixt the two drives, over and over and over and over).
I would bet that USB and TBolt use a common library and that library has issues. From past experiences, don't expect Apple to acknowledge this issue, nor address it with any urgency (it's ONLY you're data, right?). If you have a USB device you are currently using as a backup device, I would stop using it until the issue is resolved. If you have a backup device and there is another Mac on the same network, I'd transfer the device to the "properly working" Mac and then access it via File Sharing. It's slower, but infinitely safer than improper disk ejects.
One saving grace is that the Mac file system is "journaled" and has a much better chance of recovering from a disk error than any Windows system.
I have the same problem with one of my two Seagate 8TB USB drives. Both are connected to mi M1 iMac via an ANKER hub. The drive I use for TimeMachine has no issues. The other one I use for media files keeps popping up the "Drive Not Ejected Properly" message every time the computer wakes up. Per Seagate suggestions, I checked the cables, switched ports on the hub, set the energy settings to "Prevent you Mac from automatically sleeping", not "Put hard disks to sleep", and "Wake for network access". I also repaired the drive which needed repair. Seagate suggested that the not ejected warning would pop up if the disk needs repair. The disk did need to be repaired. This worked fine after the first awakening. Then it resumed popping up the notification. It turns out that the disk needed repairing once more.
Any suggestions?