I just had hardwood floors installed in my kitchen. They are Select Red Oak finished with three coats of Fabulon polyurethane.

Two days after they were finished I dropped my metal level on the floor.

UGH!

It dropped from the kitchen counter and the corner of the level left two deep gouges in the floor.
One is about the size of a nickel, the other about the size of a dime.

I called my the company that did the installation. They suggested applying some Butcher's Wax to the two areas. They said I can get it at the Home Depot.

The gouges are not terribly conspicuous. When we put the kitchen island back, you probably won't even see them, cause the island will cover them.
Therefore, I am not too worried about aesthetics. I just want to make sure the floor is protected.

Any suggestions on repairing these gouges/scratches?

Go to a local distributor of hardwood flooring supplies, one that sells Woodwise products. You want to buy Woodwise Prefinished Floor Putty/filler.
http://woodwise.com/woodfiller/prefinish.html
It comes in many colors so find the one that matches your flooring. Apply the filler/putty with a plastic putty knife and let dry. LIGHTLY sand filler flush with very fine sandpaper (220), dust off and apply a coat of poly that matches the sheen on your floor. Just coat the area that needs it.