When the web server runs it reads files as your username (ie myuser). So pretty much all your files will be created with this in your home directory.
php however uses the user nobody for all it's file operations. fopen, mkdir, chown, chmod, etc. So if your creating files from a php web page it will create the files with the user nobody. This means if you have SSH or file manager it may be impossible to access the file if the permissions are 700.
Now that these files are created if your web page loses track of them their impossible to delete without using a php script or getting the tech team to delete them as root.
So if you run into files you can't clean up. This could be your problem.