Looks like the Xfce forums to me. 
Like they mentioned there, the error should not affect functionality. I wouldn’t worry about it.
No, don’t go messing around with system files.
❯ pamac search ---files /etc/X11/xinit/xinitrc.d/80xapp-gtk3-module.sh
/etc/X11/xinit/xinitrc.d/80xapp-gtk3-module.sh is owned by xapp