This is an issue with Unity in general - it's not a problem specific to AC.
In order for a character to react to a NavMesh Obstacle, that character must themself have a NavMesh Agent - as well as a NavMesh Agent Integration component for AC to work with it.
However, you may be able to get away with simply checking Carve on the NavMesh Obstacle component, so that it updates the NavMesh itself. Try playing with the carve values and viewing the blue NavMesh in the Scene window at runtime to see what effects they have.
Comments
This is an issue with Unity in general - it's not a problem specific to AC.
In order for a character to react to a NavMesh Obstacle, that character must themself have a NavMesh Agent - as well as a NavMesh Agent Integration component for AC to work with it.
However, you may be able to get away with simply checking Carve on the NavMesh Obstacle component, so that it updates the NavMesh itself. Try playing with the carve values and viewing the blue NavMesh in the Scene window at runtime to see what effects they have.