Wood filler didn’t stain the same color as the wood

Q: My husband and I bought an old home (over 100 years old) and it has all original hardwood floors (this is the subfloor). There were a lot of gaps and nail holes where the boards were facenailed. We decided to fill in the gaps and holes with wood filler. We sanded the wood filler down and stained the floors and the wood filler didn’t stain the same color as the wood. It left all the areas the filler touched discolored.

I’ve seen on a lot of other sites what we could have done before staining or adding the filler, but we’ve already used it, what can we do now? How do I get a wood filler stain match? Add more stain? Resand and stain?

A: The wood filler probably has to be sanded to break the hardened surface to accept the stain. It is possible it shrunk so that when you sanded you didn’t actually touch the filler at all. How many nail holes are we talking about here? Could you apply a coat of finish and then use a colour matched tube filler such as Color-Rite to touch up the nail holes? It seems a huge waste to sand it all over again. I think I would get a coat of finish on the floor and then try and deal with the filler. The coat of finish will keep the filler residue from sticking to the wood surrounding the holes. You could even use Woodwise or equivalent and fill the holes with a putty knife. Fill the hole and wipe off the residue with a damp cloth. Then go around and touch up the filler with stain.

Related Q: We had our 25 year old floors refinished in late September. This problem began showing up in November, and just keeps getting worse. The floors almost look worse than before they were refinished. To me there was some reaction with the filler they put down and the poly? (Picture attached.) Also noticed all these small scratches. This poly just doesn’t seem as hard as the old poly. And it’s just my wife and I, we are retired and are in socks or bare feet the majority of the time. Any idea what caused this? Is there a cure other than refinishing?

A: Were those small gaps that light when they first stained the floor? I ask because filler does shrink and when it dries it gets a skin over the top which has to be sanded off to accept stain. So, if the filler shrunk down and the final sanding didn’t remove that skin the stain would stay light and not accept the stain. But, if that was the case, why wouldn’t they try to fix it then before proceeding? I can see spots where the filler has shrunk and cracked, which is rather normal. But then there is another spot where the filler looks intact and smooth, but it has not taken the stain.

There are stain pens that might work to darken these up. It’s a pain, tedious, with no guarantees. A bigger concern is the scratching, given there are no big dogs and seldom shoes worn. It makes me think that a good bond has not been achieved between the coats of finish. I’m surprised it isn’t peeling. If the other coats are sound, a good screening and re-coat should help a lot. If there is an issue with adhesion, likely through insufficient preparation, the job would have to be done over.