It seems like defraggler can't list all the files on non-system drive, thus leaving several stray files untouched.
I can't figure out why it does that. There's nothing wrong with file permissions/ownership, path of the files, files are not being opened by system, they are not metadata files, they are not alternate data streams....
It has trouble reading/cathalogizing files in random folders. Moving the folder seems to jolt something and once again defraggler can read the contents of it.