Problem with destination when I copy a files ...

For some time, the plugin is not working properly.
When I put a file / files (graphic, pdf, other) to the selected directory, the files first goes to the main directory (not to the folder) and then later I have to move it manually to the corrected directory.
It should be like this: files should immediately go to the specified directory.
Can anyone help me ... please.
I manage a large site, every day I copy 100-500 files per server, through the WP Media Folder plugin, and it's a big problem for me.