Normal to see staples in hardwood floor? If not, how best to handle/fill?
No, that's not the normal way to fasten hardwood floors.  Usually they are nailed or stapled on the edges which are then covered by the adjoining piece.  I suspect there was a problem here and the flooring was raised up and rather than take it out and do it right, they just stapled it down and left it.

Poor workmanship in my opinion.