Here is a picture.

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Stain bleed back, must be Minwax stain. It should have been wiped off before applying the topcoat.

It looks like the wood was number two grade selection, and when they refinished it, they did not reapply the wood fillers.

What was the colour of the floors before you had them refinished? What is the colour/finish now? How many coats of finished used?

I'm have the same issue and wondering if you ever figured out the cause. I only noticed it after the top 3rd coat (oil based finish).

wow sorry to hear. I have it in just a few places mostly in the center of the rooms , this is new red oak wood in bedrooms with an oil poly finish, they waited 24-36 hours between each coat so not sure that was the issue. They are trying to tell me that it may be the wood. See attached. Thanks for your reply.

That looks exactly like the issue I had except I had it everywhere on all my HW floors. The flooring inspector said the times that appear on the labels of poly are those determined under lab controlled conditions and that a refinisher should evaluate conditions in a home before applying each coat. If what you are seeing is pinholes in the finish, I can tell you from experience that adding another coat of poly will not fix. My original contractor put on a very heavy 4th coat (I had yellow lines on all my baseboard trim 1/4 inch high). The 4th coat took 2 full days to dry and all the pinholes were still visible so I would not recommend putting on more poly to fill in as that doesn't seem to do the job. I was told over and over again by the contractor that it was my wood. However, when another company came out and sanded and refinished a 2x2 ft area in a closet it was clearly apparent that it was not the wood and that it was the finish because all the pinholes that had been there were gone. Temp and humidity and other factors can affect how long it takes poly to fully dry per the inspector who came to my house and he noted that relying on time only before applying subsequent coats can result in finish issues in some cases.

Those pinholes is stain bleed back. Certain brand stains will bleed back. Minwax is one of them. Poly will not bond to wet stains. The only fix is to sand and re-stain, then allow the stain to completely dry however much time that may be.

Thanks G&S floors, thanks for your reply. can it really be stain bleed back if this was a new red oak install not a refinish job? Also the floor company stained with duraseal and then applied 3 coats of oil based polyurethane. First was satin, 2nd and 3rd was matte finish. I didn’t notice the pinholes after the 2nd coat only after the 3rd.

My floor contractor tried to tell me this happens with the oil based matte finish and that they can sand and 4th coat with satin.

It's the ingredients in the stains that causes it to bleed back. When a product causes bleed back, going over it with a polishing pad helps remove any additional excess finish. Bleed back will occur with stains, penetrating oils and hard wax oils, not polyurethane coatings. To prevent it, use a better quality finish.

Polyurethane coatings will cause poly beads, usually in the joints, when the conditions is high humidity.

Pin holes in a polyurethane coat can also be caused by a contaminant that splattered on it, causing the chemical reaction. This can be water, silicone or a wax based product.