After a reboot, all icons on my desktop where displayed 2 times, although only one copy of each was "functional" in that I could drag it around.
The bad duplicate seemed just to exist in the background. Searching the internet did not turn up anything of interest, so I grep'd the various settings that gsettings offers. My first idea was to set gsettings set org.gnome.desktop.background show-desktop-icons false, which temporarily solved the issue, but only temporarily. After the next boot, the desktop was completely empty, so I set it to "true" again.
The solution was gsettings set org.nemo.desktop show-desktop-icons false, which removed the "bad" duplicates and only left the clickable ones.
- Debian 9.0
- GNOME 3.22.2
- Kernel 4.10.17