Characters with NavMeshAgent attached will collide with each other.
For example, create a prefab that has a NavMeshAgent but no Collider, RigidBody, or NavMeshObstacle.
If this prefab is created in succession at the same point, the characters will collide with each other.
I tried to prevent the layers of this prefab from colliding with each other in Physice, but it did not improve the situation.

