These are emergence holes made by adult beetles leaving the wood.
Poly wood floor has holes.
There are many different types of wood floor fillers.
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.
Some are designed for general application where others are more specific.
Remove the excess wax and buff the floor.
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.
I have seen what you described many times.
Now back to the floor.
Most hardwood floors have been dried and aged but were part of a tree and then board at one time.
New flooring is installed and finished and then months or even years later small holes develop.
Polyurethane hardwood floor finishes come in two varieties.
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.
Apply a light coating of floor wax to shallow scratches using a soft cloth.
Alternatively use a touch up polyurethane repair kit following manufacturer.
All hardwood floors get filled during installation sanding finishing and use.
All polyurethane finishes are water resistant but flooring professionals advise using water sparingly if at all for cleaning.
Those from the factory and those applied on site.
Don t ever wax a wood floor that has been coated with a polyurethane finish this will make it impossible to re coat in the future without having to sand the floor first.
If you take a close look at any prefinished wood flooring right out of the box you will see that it has been filled.