This is pretty awkward, and I saw this on XFCE too, so here goes.
I installed MATE desktop using sudo apt-get install mate-desktop-environment and, the x-caja-desktop (found that out by killing mate-panel) will not fit the whole entire screen, leaving the unboxed area non-clickable (can't touch any files).
The picture below was taken after my attempt to do "dconf reset -f /"
I just tried reinstalling it with that, didn’t work. However, when I tested it on Ubuntu 19.04 Disco Dingo Test Build, the issue didn’t occur and I think I did do it once on this OS, but then after reinstalling it, it came back so I will take a look into this.
After a fresh reinstall of Ubuntu 18.10, it was good. It was probably because the ubuntu-mate-package tries to hold lots of other crap, so when uninstalling its good to use sudo apt purge and when installing, --no-install-recommends flag.