I have gone over the filler areas with a furniture scratch touch up pen, trying to darken and make it blend in. It's kind of fun in a challenging, fiddly way.

I have used the kind below but I am sure their are many out there. it's just stain in a pen applicator, afaict.

Here is a link that might be useful: touch up pen

Not a bad idea (and thanks for the link), especially since I cringe at the idea of painting over so much beautiful oak! I'll give it a try unless anyone else has a better suggestion?

Those pens contain stain -- lots of thinner, dye and/or pigment and just enough binder (varnish/oil) to hold it together until top coated. It will quickly rub of unless you top coat,

In the future, it's better to do the staining and finishing, then come by with a wax filler on the nail holes. Stainable filler is an oxymoron. Yes, fillers take stain. But they also block stain from the surrounding wood and never take stain the same as the wood.

"pore filler" is a very different animal than typical wood fillers for holes and defects.

Pore-O-Pac is Behlan's name for their paste wood grain filler.

It is very fine silica in a binder and used to fill the actual wood pores in woods like oak to produce a smooth surface.

If they used grain filler the entire surface should be covered, not just parts.

If they used a wood filler for holes and defects they are ALL notorious for not taking stain the same as the surrounding wood. Like glue spills they prevent stains and dyes from penetrating uniformly and producing a uniform color.

Sanding the finish off and then using a colored top coat is probably the most effective way of fixing the problem.

Just avoid polyshades. The pigments settle out even as you are applying the stuff producing uneven color, and vigorous shaking or stirring can produce bubbles that affect the final finish.