This is a major pet peeve for me. Funny story: in one session i had, the director was jiggling his foot during a scene, which was causing the chair to squeak a little. Afterwards he said "i don't know about that bird, can you take it out?".
But in all seriousness, it's easy for an inexperienced (and maybe experienced) director to become attached to what they did or didn't hear on set, or to the guide track that they've been listening to throughout the picture edit. Then, when they notice something new that they hadn't expected, they can be automatically resistant to it.
Mainly, i think that if they're noticing it, perhaps i haven't integrated it as well as i could. Ideally, if i've done it right, the director will feel the effect it has and welcome it, rather than have their attention drawn to the sound effect itself.
On the other hand, maybe they're focusing too hard on listening, instead of feeling the ebb and flow of tension/mood/emotion and whatnot. In this case, i'd explain what my intentions are for the sound, and the thought process behind it. Then, maybe, they'll be more receptive to the effect that the sound has, or perhaps we can then come up with something the director likes, which has a similar effect.