If, it is repeatedly in the same spot. It's most likely part of the feature in that particular board. The other cause would be metal filings that were not completely removed. A water base finish will cause a rusting reaction with metal filings, shavings or dust. These stains can be difficult to remove with sanding. The penetration depth is unpredictable.

Thanks for the response. But it happened in several places...not only one board. And after applying the sealer, the stains go very easily with sanding...I tried to apply the sealer on different sections of the floor, and I get those black spots here and there...

What do you mean by metal fillings in the board? how did they get there? Sorry is this is a stupid question:)

Any equipment or items that are made of metal that has a rusty spot will produce metal dust. The dust is so fine, it is not visible to the naked eye. Any of the dust that gets on the wood fibers will rust , when it comes in contact with finish.

Someone might have transported an appliance or something. Or someone was filing or sharpening a piece of tool. It could have came off someone's clothes or body. Soil from outdoor will cause these types of spots. Post more pictures of these other spots. I would like to see the shape.

It can also be mineral streaks in the wood. Which is a natural attribute of the wood. As I mentioned earlier.

Here are a few more photos from different planks

Do they return when the floor is sanded properly and then coated?

This is a newly installed floor. I no longer trust my installer, so I stopped the work and I am now trying sealers on my own. I only sanded the floor unprofessionally, with a small hand machine and a sanding paper, but those marks were not there before, they appeared after I applied the sealer and they go away easily with further light sanding. I never checked humidity, and neither did my installer. But I keep the AC on all the time and the floor is now about 1 month old.

I will try to sand and put a second coat and report again ASAP

Thank you all

What's your applicator? Just trying to figure out what is causing these black deposits.

What happens if you sand down but do NOT add sealant (leave it dry and bare)? What happens if you sand down and apply WATER only (same application technique but only water)?

These are two simple ways of adding in TWO control groups. The 'dry group' is one...the WATER WET is going to be the 'tell all'.

Photo of the applicator?

What is the product that you are applying? Is it possible to sand a spot to raw wood and post a picture to be analyzed?

I used a paint roller to apply the Bona Natural seal. When I hand sand them, the marks are removed quite easily (see photos). Then I applied water only with the same roller, and the marks are back - though less prominently than before

These are the marks after I applied water only (after light sanding and removal of the black spots). The spots are back, but less dark than before

There isn't much you can do. It's the boards itself. You can replace the individual boards affected. I would just buff it and apply the poly. The poly doesn't cause bleed back like the sealer, since it is design to sit on top of the wood fibers.

IMO it is in the wood and you either replace the boards that give you this or just leave it and honestly most people will never notice after all done and furniture moved in . IMO though you need a pro to refinish your floors.