So I have been having the same troubles with ejecting my USB drives ever since the El Capitan update also. I think you guys have found a work-around by going to the privacy settings and preventing spotlight from searching the drives. This is a good one that I will try, but I found this error the hard way one day when months of research on an encrypted iron key thumb drive was at risk. I took it to Best Buy and a guy pretty high up in the Geek Squad plugged it into his windows computer. The Geek Squad at Best Buy runs a proprietary software created in-house that apparently removes all permissions/restriction/limitations on files (for example I had one instance where a file kept asking me for an administrator password that I somehow must have linked to the thumb drive saving stuff from a computer at the hospital). When he checked the drive there were hidden files that I didn't even know about (.DS_Store, .Spotlight-V100, .TemporaryItems, .fseventsd) apparently these are files that the mac puts on the computer so that it becomes accessible to Spotlight. So we both found the problem just from different ends of the problem. My issues still are multiple and if you guys have an answer that would be awesome.
1. If I use my thumb drive at home on a macbook pro running OS X El Capitan but also have to use at work which are mostly windows based PC's that all require me to log-in my own "windows" and I'm not the administrator level, then what is the best way to transfer files to/from the thumb drive and the PC's and my mac without running into these issues?
2. There seems to be a difference when I drag/drop a file vs when I copy a file then paste a file to the thumb drive. The latter seems to be the preferred method, because the drag/drop method seems to "connect" the file. This is just from my experience and I'm not a computer whiz, just from hours and hours of dealing with this since the El capitan update.
3. If I proceed with the work-around by preventing spotlight from searching the drive, do I have to delete these hidden files before this work-around will work? Which of these hidden files can I just delete without corrupting the drive? This is such crap that these added hidden files are reeking such havoc on my thumb drive and my life right now. I can't use dropbox/google drive at my work because they are blocked by the hospital software, or I would just do this. I have to use a hospital approved iron key that encrypted or I can't use a thumb drive to save my work. Ive searched for getting rid of the above files and keep getting crazy stuff like renaming folders/files (http://apple.stackexchange.com/questions/6707/how-to-stop-os-x-from-writing-spot light-and-trash-files-to-memory-cards-an…) and it starts to get over my head pretty quickly and get into stuff that in my hands could compromise the whole drive. It's gotten to the point where its difficult to even use a thumb drive on my mac and I find myself emailing files to myself and have to keep remembering to download them and add them to the thumb drive while I'm at work.
Any help would be amazing (Kicking myself for downgrading to El Capitan)