The first coat of finish will show flaws that weren't visible before. The middle picture is quite typical of an old urine stain. They often extend all the way through the wood so the only fix is to replace boards. Google "urine stain on wood floor" and look at the images.

The top and bottom picture could be something else but I suspect they are from something the floor had prior. The only exception is the faint diagonal line top middle of the third picture, which could be tannin pull. If it was worse and the floor was near perfect I might take issue with it.

Many years ago, as part of a large refinishing job, we tore up layers of kitchen flooring and finished the old Pine beneath. I was quite pleased with the way it turned out, considering the age and that it had been covered by other floors and probably subjected to leaks and hurricanes. The owner was disappointed because she saw the floor before it was sealed and thought that my finisher had applied something that caused irregular blue green stains on the floor.

What did your floor look like from before the sanding started? Do you have pictures?

We will need to see before images of the floor to help determine cause. It looks like pre-existing flaws.

Loba invisible does not cause tannin pull and stains. The first coat can have lap marks, but it disappears after the second (final) coat is applied.

I have to agree that these were preexisting but almost invisible because of the sanding. The top pic looks like "old finish" was left in place. Considering how thin your boards are and how old they are, this is not unexpected. And to be clear, old floors can have 80 years worth of contamination (ie. wax, shoe polish, Pledge, Murphy's Oil soap, soap, hairspray, hair dye, etc) on them. These products can, and will, get past the original finish and contaminate the wood. Just like old urine stains pushing all the way through a board (the dark gray stain is most like an old urine stain...cause that's what they look like after many years), these contaminants can go several millimeters into the wood. Especially things like cooking oil, Murphy's Oil soap (anything oil based really) or even melted wax from a candle.

After sanding, you wouldn't have 'seen' these things. But a quick swish of a slightly damp mop (make it wet to give some depth of colour) and all of these things would have been evident within moments of the water touching the wood.

And that's why you can see them now. The clear coat is like water hitting the wood. It gives the colours depth...and definition. But unlike water, the finish is permanent.

At this point, I would keep going with your plan = 2 more coats of Loba 2K Invisible. And You will want to hurry. To get a good 'stick' the next coat should be put down within 24 hours of the previous...or else the flooring guy has to abrade the floor again to get a mechanical grip rather than a chemical stick.

Keep going. Know that you are getting 20 years more out of these floors that probably should have given up the ghost 20 years ago. That means you are extending the life by 40 years. For an old hardwood floor, that's impressive.

Ugh SJ McCarthy - I am going to be behind the 8-ball on continuing with the clear coat plan- it's already been 24 hrs and I'm going out of town tomorrow for five days, so nothing will happen in the meantime :/. The contractor kept saying the stains would show through no matter what, and that I need to go to a dark stain or I wouldn't be happy, etc. And he kept insisting that my dog had peed over the entire floor overnight, causing all the stains, which this crazy insistence didn't help the situation. (To clarify: We have only lived there six months, and my dog doesn't urinate on the floor, although these could certainly be old stains from another dog) The contractor also said he tried to scrape the stains and smelled them, and "they smelled like urine". I asked him to perhaps do a light sanding and continue w/the clear coat, and he said, "The stains will still be there" "Then what?" "What's the end game?" "You'll never be happy" "You need new floors". Lets just say the conversation didn't end well.

Also, he got very angry when I calmly asked why the new maple floors from the kitchen that he put in didn't match (size, not color-see below) He said I should have replaced the old maple floors (on the right side in first pic, left in second) and he thought it was odd I didn't want to rip them up. I didn't replace them bc everyone said they could be matched, and why tear up good, old wood floors?

Below is the stain from a different angle. I'm not as worried about the dark spots as the yellow. I'm wondering whether the yellow could be lap marks like G&S Flooring mentioned? I know the worker was slapping it on pretty thick and not smoothing where it accumulated. And there is only one coat of Loba on there, so we never got to a second coat to see if it would disappear - the contractor kept insisting they wouldn't. I'm just not sure if he's familiar with this product on un-stained floors.

And for your reference are some old photos of the floor - sorry I could only find ones where it's covered in dust from construction, and then one where you can only see slivers of it from under the rug and furniture. But hopefully gives some more insight.. Thanks guys - I love getting your feedback!

These floors look like 3/4" thick flooring, based on the last image. Did you measure the wear layer to see the actual thickness of it? I do not see any indication of fasteners being exposed, if, the wear layer is too thin to sand. You probably have plenty of life left in thee floors. Find a gap in a joint, stick a business card down to the top of the tongue of the floor board and make a mark with a pencil or pen, then remove the business card and measure the mark. You will know how much life you have left. The wear layer cannot be less than 9/32. If, it is, then you need to replace the flooring. A complete sanding (rough and finish) removes 1/32 of material.

Your floor looks like yellow birch, not hard maple. To confirm that it is hard maple. Look for boards with curly (wavy grain) or bird's eye (a bunch of little circles shaped like bird's eye) configuring.

The second image of the last four, looks like a different specie.

The 'before' pictures suggest that the stains you see now would not have been readily evident before refinishing.

I suspect G&S might be right in that the other floor looks like Birch. Hard to say why the widths don't match but currently wood is generally made to specific dimensions by all manufacturers. If someone makes 2-1/4" wide wood it will be very close to 2-1/4" wide. They don't make standard 2-3/16", 2-7/32" or 2-13/64" wide material in anticipation that you'll need it. If your old wood is slightly narrower, there will be a slight mismatch. How wide are the old floor boards? What's has the floor been subjected to? Could it have expanded and crushed the grain at the edges of the boards effectively making them narrower? How wide were they when they were new? In any case, you're patching an old floor. It's extremely unlikely that it's not going to look like a patch. If you don't want a patch, pay for new.

Since we only get one side of the story I'm not going to make any pronouncements, but you might consider that the floor person is keying off what you're projecting. You state it's an 1880s house yet seem disappointed that the flooring has flaws. The floor person may be keying off your dissatisfaction. We do work in older houses here (not 1880s!) and generally the owners recognize that they're not going to be perfect. I'm indelicate enough to point that out when people forget it. Consider that you're looking at the floor with no rugs, furniture or window treatments. Once it's put back together I suspect that many of the flaws will be covered and you'll get used to the rest. At some point you can replace the floors and they'll be perfect, for a while.

Where do you find the loba 2k invisible?