How do I make AI objects not walk on top of each other?

Have you tried adjusting the stopping distance of the NavMeshAgent components of the characters?

http://docs.unity3d.com/ScriptReference/NavMeshAgent-stoppingDistance.html

If that's not enough, you could add a script component that uses the onTriggerEnter method that will GetComponent(NavMeshAgent).Stop() when it detects a collision with another navmeshagent gameObject collider.

http://docs.unity3d.com/ScriptReference/NavMeshAgent.Stop.html

Hi @dubstaphone,

I have the same issue, did you solve it? I've been trying changing Rigidbody values (Mass, Drag, Angular Drag) but nothing. I hope you can help me somehow.

Thank you!

Try changing character controller' Steop offset to 1

Unity is very poor in this regard, best to get rid of physics interactions between moving objects altogether and do your own, you can try all things everyone suggests and believe me, nothing will work, you should just use Triggers and Raycasts and put them on layers that don't react to each other on the built in physics

For me worked to lower the "Slope Limit" stopping the "character Controllers" to climb on each other.

Sometimes you also have to increase the "Capsule Collider".