If one's updating from gnupg 2.0.x to 2.1.x, there's nothing in the latter's Makefile to make it conflict with security/dirmngr, which is a runtime dependency of security/gnupg20.
Which means that the upgrade only fails at the end:
===> Registering installation for gnupg-2.1.0_1
pkg-static: gnupg-2.1.0_1 conflicts with dirmngr-1.1.0_12 (installs files into the same place). Problematic file: /usr/local/bin/dirmngr
Auto-assigned to maintainer kuriyama@FreeBSD.org
Fix committed, thanks!