I believe by default these folders are created by user interaction, however, it’s possible that a plugin may be calling a function to create these monthly upload folders.
Note that using this function will create a subfolder in your Uploads folder corresponding to the queried month (or current month, if no $time argument is provided), if that folder is not already there. You don’t have to upload anything in order for this folder to be created.
That’s according to the the Codex > Function Reference > wp_upload_dir(). Maybe you could get more detailed logs to determine how they’re created…I’m not real familiar with server administration.