I had some water staining on my 50 year old oak wood floors. The stain wasn't deep and i was able to sand them out. When I refinished the floor with the poly the flooring contractor told me they used when they refinished the floor a year ago. However , those spots came out grey (even spots that hadn't had water damage) when I applied poly, as opposed to the tan red of the rest of the floor. I don't think they used any stain. What could I do to match the color better, does it need a sealant or something?

https://docs.google.com/document/d/1Cj_ ... p=drivesdk

Pictures of floor

You may not know all the history of the floor. Have any pets been allowed on the floor? When a floor gets another coat of finish it gets brighter and shows the color of the wood more. It looks like you have some old pet stains.

I would think it is stains too, but the sections around the shallow stain that I removed are also grey, it was a raw wood color and as soon as I put poly on it showed as grey instead of reddish. I wasn't sure if water popping or sealant was needed, or if I was missing something else.

A coat of finish acts as a seal coat. Water popping will not affect the color unless you are using a stain color. It just raises the grain so more stain penetrates.
If wood is exposed to the atmosphere it will become gray on the surface, so worn spots become gray if the finish is worn off and then coated with finish. This usually happens in doorways where there is a lot of traffic. You have stains that are not from finish being worn off then coated. Urine stains will darken the color to a gray color and then black after more has penetrated the finish. Urine will also turn most finishes brown before the urine penetrates into the wood.