We've had some issues with PDF files in the Media Library. Once a file is uploaded (while writing a post, we choose an icon to upload media into the Media Library, and then upload a PDF file from our computer), and then removed in the Media Library management, it does not always disappear from the wp-content/uploads folder, but it disappears from the Media Library.
Uploading a new file of the same name then makes the new file named MyFileName1.pdf - adds the 1 at the end.
We have to FTP into the uploads directory and actually remove the old file and then the new file from the Media Library, and upload it over into the Media Library once the original file is gone for it to upload correctly.... so the issues is the file is not actually deleted in the first place when removed via web interface.
If it matters, some of the files in our uploads folder are user:group like apache:apache while others are our ftpaccountname:psaserv
The ones that are an issue are apache:apache. But that's Media Library uploads are all apache:apache ...
The uploads folder is drwxrwxrwx permissions if that makes a difference.