My newly installed red oak floors have a number of small black holes in them. Some of these I assume to be nail holes; they have been covered with finish, are not terribly conspicuous, and are not palpable; these I'm not concerned about. But others are palpable holes and give the appearance, at least, of having been made after the top coat of finish was applied. I wanted to add photos but not sure I'm going to be able to figure out how; just clicking img is not giving the option to upload anything. If I do manage to add the pictures, are they all just nail holes? What, if anything, should I ask my contractor to do about them?

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The standard of the industry is to set nails if necessary and fill nail holes.
This is easily done before the last coat of finish. After the finish coat, putty can
be used, but sometimes gets dirty and is hard to clean, if not protected by a coat of finish.
Special "pre-finished" putty can work the best made by Woodwise.
It dries hard and keeps it's color.