Hello Nancy,
Yes, this does appear to be standard behavior. I think the reason why there are subfolders is that with the new moodle 2 file system, any file that is added to an activity or resource permanently belongs to that activity or resource (i.e. it's copied to that activity or resource). And so any activity or resource now has its own internal file structure.
For example, in the above screenshot I can see that you've added five 'file' resources to a course called 'Moodle 2.0'. Each resource has its own directory called 'Files and Folders', which in your case contain just one docx file each, but they could contain more files.
I've attached a screemshot of one of my courses in which there is just a File resource and a Forum activity. You can see a similar file structure.