Welcome to the community, @bossnec. For future reference, questions on how to use AC belong in Technical Q&A.
You haven't said how you're controlling the player, and this is important as it affects how your NavMesh affects the player. Are you moving him directly, or is he attempting to pathfind to a point on the NavMesh that's inside the cube? A shot of your Settings Manager will also help.
Generally though, you will want to make sure that your NavMesh does not cover areas that the player cannot move. If you're using Point And Click movement, you don't need to use colliders - only rely on the shape of the NavMesh.
It looks like you're using the Mesh Collider pathfinding option, is that correct? If so, you will need to make a new mesh that accounts for the objects that can't be walked into. Blender was used for the 3D Demo's NavMesh.
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