Usually this problem means that the var XDG_DESKTOP_DIR got somehow set to $HOME instead of “$HOME/Desktop”…
FIX: Edit the file ~/.config/user-dirs.dirs and fix it:
XDG_DESKTOP_DIR="$HOME/Desktop"
… typically this file should look like this:
XDG_DESKTOP_DIR="$HOME/Desktop"
XDG_DOWNLOAD_DIR="$HOME/Download"
XDG_TEMPLATES_DIR="$HOME/Templates"
XDG_PUBLICSHARE_DIR="$HOME/Public"
XDG_DOCUMENTS_DIR="$HOME/Documents"
XDG_MUSIC_DIR="$HOME/Music"
XDG_PICTURES_DIR="$HOME/Pictures"
XDG_VIDEOS_DIR="$HOME/Videos"