I am not sure if this is a bug but, when I create a new website, the owner of the site folder is root:root. because of this I cannot create subfolders directly under site folder. But I can create folders under "site/web" folder. to overcome this I login as root and change ownership of site folder. I also used IspConfig2 before it was not working like this, site folder was owned by the client.
Thats correct. Thats intended and had been changed for security reasons to avoid the possibility of symlink attacks. Folders created by the client have to be inside the web folder. In ISPConfig 3.0.5 there will be also a folder named private were a client can create folders.
