If, the stain on the stairs is Special Walnut and the botom floor is the same color. Then , yes, have them redo it. Have them water pop before applying the stain.

If, they did water pop. Then they installed the wrong specie and the floor should be removed and replaced with white oak.

SJ - He did offer sample patches - on the upstairs floor which is the same color as the stair treads in the picture, not on the downstairs floor. Needless to say, I was expecting it all to look the same.

After I posted this, I recalled that the flooring contractor did install a few new boards on the first floor because I tore down a small portion of a wall. That new portion is the same color as the flooring around it, so I now really think it isn't necessarily the type of wood but instead a different color of stain.

So which floor matches? Does the upstairs match the stairs? Or does the upstairs match the downstairs? Do the stairs stand alone as a weird colour?

How old are the original floors? Are they close to the 20 year mark? If so, is there a reason why they were not refinished at the same time as the stair treads and the upstairs?

The upstairs matches the stairs (this is the color I selected), and they were all just refinished a week ago (all at same time). Shouldn't they all match? Not really sure how old the downstairs floor is...

Ok...so YOU selected the finish. Right. Now we have a better understanding of what is going on. The wood the REFINISHED touched matches (each other). What does NOT match is the old (which the refinisher did NOT touch) and the new (which all matches).

So the question becomes...who decide the stain UPSTAIRS was going to match the DOWNSTAIRS?

How close did you see the patch in relation to the existing floor? Was it on the 'bottom step' or was in in the 'main bedroom" (like 500 feet away)? He who signed off on the sample holds the answer to "Who's responsible?".

No, all the wood was refinished at the same time - the downstairs, the upstairs and the stairway. The refinisher touched all of it in the same job, but stained the upstairs on a different day than the downstairs. I selected ONE color for ALL the floors and they all were supposed to be the same.

And then the next question: did the contractor match the species? Did s/he send away a sample of the original floor to a lab? This is the last 'weak' spot for a single stain having such a large colour difference.

After that, it is on the contractor to explain the colour difference....and correct it.

Sounds like you did everything in your power, now it is on the contractor to resolve and make them all match up as well as possible. If you run into trouble, are you planning rugs and runner on stairs? If so, you might be better off leaving well enough alone. Sometimes "fixes" can turn out worse than original problem, plus you loose some of the surface of the woods? Your call obviously. While they definitely don't match stair treads and flooring at bottom of stairs, they don't look horrible either. Just bad given your expectations. Sorry, hope you can get it resolved.

Stairs looks like white oak. Your main floor is red oak. The red oak floors do not look like it was water-popped, whereas the white oak is. Water-popping would get the colors close. Only notable difference would be the red oak would have a red hue, but still close.

It's either that or the sanding process is different between the two areas. They closed up the grain of the main floor, did not use water-pop process and the two different sanding takes the stain differently with the main floor resulting lighter. But once again, water-popping would alleviate that issue, even if, you were two grits off. Example: 100/150 grit.

Possible chance they did not stir the product well enough or at all.