This happened in bug #412881 with Munin, which has this dep: dev-perl/net-server[ipv6(-)?] The stable version for x86 of dev-perl/net-server wouldn't work because it doesn't have ipv6 USE flag at all, but repoman does not complain.
This is fixed in git: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=ca79d9994fc43909203daad5f2c12f750a504b28
This is fixed in 2.1.11.18 and 2.2.0_alpha129.