The sanding process should remove those marks.

Odd. At first glance with my aging eyes, I though it was a piece of quartersawn. Off to happy hour.

Your installer isn't much of a craftsman. He could have culled those pieces if he cared about the look of his work. I'd replace that.

It's normal, natural water marks in the wood. Sometimes those marks are more pronounced. Most commonly found in rift and quartersawn or quartersawn wood. It's barely noticable after coating is applied over it.

I have that on a couple of my stairs. My floor guy stained the one stair way too dark so I of course made him re-sand and stain it. He did not explain at all why he did it that way. When it was bare I saw the marks and he told me that was why he stained the stair dark. I of course, thought he didn't sand well enough and made him sand it a yet again. If anything the marks got darker. Weirdest thing I ever saw. I told him to stain it like the rest and now... I can kind of see it in strong light but on a daily basis it is not visible to me.

If my water marks were as defined at yours I would have made an ass out of myself with the floor guy swearing that I saw the Home Depot logo in the wood... but I can assure you once the coating goes on it will be 90% less noticeable.