pkg autoremove works correct on my FreeBSD 10.2-RELEASE and I am using GNOME 3.16. pkg autoremove and it listed a number of ports/packages to deinstall that I know I use, such as ccache, unzip, docbook, all the linux-c6 stuff and so on. In fact, 246 packages in all.They were probably installed as dependencies of other packages. You can mark them as not automatically installed with e.g.I haven't messed with this in a while. I looked atpkg autoremoveand it listed a number of ports/packages to deinstall that I know I use, such as ccache, unzip, docbook, all the linux-c6 stuff and so on. In fact, 246 packages in all.
pkg set -A 0 unzip to make pkg autoremove ignore them.