Do animations affect the accuracy of a collider?

I have a NPC set up with bone colliders using the Unity ragdoll wizard. These are locational targets for a Physics.Raycast projectile. The NPC also has an Animator Controller.

I've been noticing that not all of the colliders detect raycast hits accurately. I have the colliders themselves shaped to the body parts as accurately as possible. But specifically the arms (upper arm and forearm) aren't reacting to raycast hits at all. The raycast just goes right through the colliders and hits the ground. And when I put the NPC in a crouch animation, I could only hit the torso collider in certain spots. Everything else, raycast went right through.

So, does an Animator Controller affect they way colliders attached to bones work? I was using an NPC with identical bone collider set-ups but it was using an Animation component instead of an Animator Controller and I didn't experience any of these issues, that I could tell.