What you allude to is something that crops up in government constantly: policies that have been developed in isolation from each other, rather than in conjunction with each other.
Here's a good illustration of what I mean. In Canada, we have employment equity legislation, just like you folks do. Our definition of the protected groups is a little different than yours, but it's the same basic idea of monitoring successful job attainment in the protected groups, and striving to assure that no group is disadvantaged by systemic or other non-merit-related factors.
We also have official language legislation that assures the presence of both official languages in government. Not just for the purposes of serving the public, but also for the purposes of supervision/management, and allowing people to be assessed, to be managed, and to work in, the official language of their choice. Both sets of policies are fine and fair, but neither is written to explicitly dovetail with the other. So, visible minority members may be obstructed from entry to federal jobs, or promotion to higher federal positions, by virtue of the lack of the other official language. That tends not to pertain to "homegrown" minority members who have received a Canadian education from kndergarten onward and acquired both languages, but may provide a substantial barrier to newer Canadians whose education was obtained largely overseas, and who may be somewhat "counter-prepared" to become sufficiently fluent in the other official language (at least speedily enough to be competitive in the federal job market). So we find ourselves in a position whereby promises of diversity can fall short because of language requirements, and commitments to language equity can fall short because of diversity objectives. Both are commendable objectives, but they don't live under the same roof very well.
Don't get me started on things that managers do to keep the volume of applicants manageable, and how that can often impose non merit-related barriers. So, yeah, it's a lot of little things that add up, many of which are in conflict with each other, when it comes to translating merit principles into concrete practices.