Stain Problem

I just build a red oak book case. I have put on one coat of oil-based stain, and am planning on putting on a top coat of a different color oil-based stain/poly. It might be an odd combination, but the end result exactly matches the oak staircase it will be next to.
There are two small spots where the stain didn't take, and they are conspicuously lighter than the rest. (dark spots look fine, but light spots just seem to jump out) I have a crayon-like stick intended to be used on scratches that is about the same color as the stain. I am thinking about using it to darken the light spots before putting the top coat on; but am concerned the top coat might not adhear well to it, and it might be worse than not doing anything. (my wife couldn't see them until I put my finger next to them)
Any advice would be appreciated.
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You used Minwax,,,,right..? I have often had that happen with minwax products. I had to carefully reapply over the light spots and not wipe it off. Then carefully add the extra coat of what ever you use next.

spots
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the
is it in a place where there might have been some spilled glue? -- Jim in NC
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the
Absolutely...even the employees at Loews admit the Minwax is at the bottom of the barrel.
I prefer General Finishes, Bartleys, and Zar stains and finishes.
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Tough sell when I see the things pa built over fifty years ago with their Minwax finishes.
All of a sudden the folks at "the Borg" are experts?
Two quick reasons why oil stains might leave light spots are, as others mentioned , contamination, or compression of the fibers. Doesn't matter what brand you use, won't overcome either of those.

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No, but if they are getting complaints about Minwax products compared to the other products like Olympic which they carry, it does not take much to suspect that Minwax products that the original poster and I had used is the problem.

True but I only have problems when staining with Minwax products and almost every time. The first 2 times I resanded the whole area and the spots reapeared larger and smaller in spots. I could touch up those spots with another brand when I had another brand available in the same shade. Retouching and wiping with Minwax yielded the same spots.
Basically I suspected my surface preparation but found that the Minwax product was always the culprit.
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I resanded and restained the two light spots. One went away, but the other is unchanged. I don't think either could have had anything on them, but I suppose it is possible. (The wood filler in the mortise joints is so ugly that a light spot elsewhere doesn't matter much; though my wife can't see that problem either.)
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