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A:
These black marks sound like "pet stains". The only practical way to deal with them is replace the boards. While they are usually seen and pointed out prior to sanding (and it isn't always possible to know before sanding whether the spots will come out) at times, if the floor is very dark the spots may not be visible enough to indicate what they are.
Some boards in lower grade wood can have dark mineral streaks, but that is not what this sounds like in your case. On the ends of the boards, is this black mark confined to the joint or does it creep several inches, for example on the surface and away from the end?
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