Why is my navmesh a 3d (taller than ground) triangle mesh? (img ex.)

Hello,

I'm trying to figure out how to set the terrain and other assets to make the nav mesh bake properly. For some reason it bakes higher than the ground in some spots, creating a mesh that's too tall, so enemies on the terrain don't move at all because they aren't on the mesh (which is in the air).

I've removed colliders and NavMeshObstacles from all the objects around this area ( the rocks). The image shows the mesh from the top (which looks almost right, but there are gaps), and from the sides where you can clearly see that it's high.

Thanks for any advice!