We had new hardwood floors put in the other day (due to water damage). It is 3/4", pre-finished oak. The guys hired from the building co we are using are not floor specialists and that is why I am questioning. The old stairs (same type of wood just a lighter color) had nail holes (filled) on the stair, but off to the sides. These new floors have wider nail holes (sm staples maybe?) and they are all over the stairs....and the filler they used doesnt match so it is very obvious. There are also a lot of holes (some yet to be filled) around the lazy susan, sink, and doorwall...those I am less worried about, but again with the filler being lighter it doesnt look great. I don't want to go to the company without knowing more about what can/should be done. Any help would be great.

If it's prefinished they probably used color putty to fill the nail holes.
Probably didn't have just the right color, decided to use what they had.
You can get Minwax color putty at Home Depot, just take a scrap piece of flooring to compare colors. Rub it in over the old putty, if they used similar putty, darker color will cover and hide holes better. Wipe off excess with a rag.

Color putty attracks dirt,and can't be cleaned. Have them match your wood to the appropriate color rite color.

http://www.colorriteinc.com

I am more worried about the amount of holes on the stairs. Should they be ALL over?

When I install stair treads, I screw 2x2 blocks to the stringers, and glue and screw the treads down from underneath. Adds a couple hrs to staircase installation, prevents squeaks and saves the time of filling holes later though, and looks much better. I've seen guys use 16 gauge finish nails- 6 per step, 2 at each end, 2 in the center. in these cases, we fill the holes with Woodwise filler, sand or scrape smooth when it's dry, and stain the filler to match wood.
They simply skipped part of the process. It's their job, I'd tell them to hide the holes. You shouldn't see them from a standing position- 3 to 4 ft away.

Stair treads...whats that? I can't remember the last time I installed a stair tread. I think it was before I bought my camera, circa 1998. No one wants to pony up the bucks for treads out here. I have a left over vertical natural bamboo tread if anyone wants it. I think it may be an antique by now.

When I was doin Lumber Liquidators work..did a ton of treds & risers,( matching Bellawood). They came in un-finished..s&f them in my shop. Route a groove in the bottom front edge of the tred, ( for the top of the riser to slip into). I would full spread the treds and risers. Nail the back edge of the tred, (covered by the riser). No exposed nail holes, and solid.

I also nail the back of the tread or if all prefinished plank and a couple along the edge but not out in the field, cept if your using strair nose. If running from bottom to top helps keep it down if you are working on top of them as you go

Stairs are fun if you can get paid for your time. Out here it runs about 100 ducats per step.

We're still installing oak treads on most staircases in new homes with oak floors, although I've been trying to get away from staircase installation.I don't mind finishing them. Hard to find the time for installation, and the builders I work with have a hard time finding carpenters who actually build level, correctly positioned stringers.Half the time I have to fix stringers before we can proceed...
We still get oak treads for around 20 bucks each,use painted white mdf on risers and skirts most times.

I like the painted riser look myself.

Talk about carpenters not know how to frame out staircases, you should see the junk we have here.

Having a picture would be helpfull. when you said new floor did you mean new stair treads? Other than that, the color is just as everyone else has said, go to home depot and pick a color (should get 2 different colors) and have at it.