Media files uploaded in wrong folder and not shown on the backend

Hello, my customer has a problem in uploading media files.
Some files are uploaded in the wrong path of date’s folders (as I can see via ftp and via link) and those files are not shown in the backend.
For example this one https://www.tarka.it/wp-content/uploads/2014/05/catologo-cucine-territorio-tarka-ed.pdf has been uploaded on 2 december 2016 but, as you can see from the path, the folders are wrong.

How can those two problems be fixed?

Thanks for helping

Marta