Most hardwood floors have been dried and aged but were part of a tree and then board at one time.
Poly wood floor has holes.
Sometimes the best strategy may be to hide them with wood stain and clear finish or just let them be and add to the character of the floor.
All polyurethane finishes are water resistant but flooring professionals advise using water sparingly if at all for cleaning.
There are many different types of wood floor fillers.
When filling nail holes in prefinished hardwood floors becomes necessary you have many options ranging from latex and epoxy fillers to homemade ones made with glue and sawdust.
Some are designed for general application where others are more specific.
If paste wax will adhere to the finish you can use it to hide scratches and the wax is available in clear honey tone or brown to match most any wood floor.
I have seen what you described many times.
Alternatively use a touch up polyurethane repair kit following manufacturer.
Oil based polyurethane has a slight amber or yellowish tint and can yellow even more over time which adds a bit of rich warm amber color to the floors if that s your goal.
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If you take a close look at any prefinished wood flooring right out of the box you will see that it has been filled.
Now back to the floor.
New flooring is installed and finished and then months or even years later small holes develop.
Apply a light coating of floor wax to shallow scratches using a soft cloth.
Polyurethane hardwood floor finishes come in two varieties.
These are emergence holes made by adult beetles leaving the wood.
All hardwood floors get filled during installation sanding finishing and use.
Remove the excess wax and buff the floor.