Is it possible to stop script-guided objects from ignoring collision?

Well, the title says it all, huh? I have a script-guided character that has the unusual ability to walk through walls. He has a character controller, and the walls have colliders. However, script ignores physics, so he can walk through walls. Is there a way to prevent this from happening?

That shouldn't happen. Are you using CharacterController.Move() to move the character?