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.