NevMesh cuts out holes for collision incorrectly with Skeletal Meshes. Skeletal Meshes with "Can Ever Affect Navigation" set to true and that have a Physics Asset are capable of causing this.
1. Open the attached file in Main
2. Press 'P' in the viewport to see navmesh
3. Move Skeletal Meshes in the scene around
Head over to the existing Questions & Answers thread and let us know what's up.