Possible Character Controller issue?

I didn't find any similar question. I'll try to be brief.

It's quite simple. I'm using a character controller and at least inside the editor, some random objects seems to be getting ignored by it.

I couldn't find any kind of relation between these objects. Most of them are static, with box colliders and no rigidbody. I had an interactable object do this today for the first time. Raycasting seems to keep working normally, but I haven't done enough tests to make sure it's always like this. I never had this kind of error in any project before, so I'm not sure where to begin testing it, besides playing the game until it happens randomly.

I always try to work with stable versions, so I'm using Unity version 5.3.0.