From the looks of it you will need to do a small amount of navmesh editing. If the area was open before hand then it is very likely that there is a complete navmesh running across it and your pen is now an obstruction. NPC's read the navmesh and think they can run anywhere on it but your new pen now blocks them so you will need to re-arrange things so that NO navmesh runs under your walls or you create the collision boxes I mentioned firstly for all your walls.
This is what is usually put people onto:http://tesalliance.org/forums/index.php?/topic/4668-ck-basics-lesson-4/
Be aware that 1. Never delete a vanilla navmesh island 2. Deleting vanilla triangles can cause errors also (but not as bad as deleting islands) 3. Tesalliance mentions working from up side down, I find it better to have no lighting or sky to get good contrast and make use of "W" toggle alot.
If NPC's try to walk via a navmesh but get blocked by an obstruction they do a little quantum tunneling to get past it.