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Hello all-
I just completed several pine projects with no issues. I took all the same precautions and used the exact same methods on this recent project (birch butcher block bar top).

First, I preconditioned wood with mineral spirits and then applied early American minwax (one coat only). I let the stain dry for at least 24 hours, at which time the color looked nice and even and so I began applying water based polyurethane. After the first coat of poly was dry there was no change in the stain appearance or quality; everything looked good (1st picture) so I applied a second coat of poly. I had to go to work for a few days. I came back about 72 hours later and all the stain is noticeably lighter and in some areas appears to have actually disappeared leaving the original wood color (2nd & 3rd pictures). Again, I have never seen this happen with any of my pine projects despite using the exact same process. Is it the birc

If anyone can explain why this happened it would be much appreciated by this hack woodworker!
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You have a few things going on which could have caused your problems. The first is the stain should have been wiped off right after applying it. If it wasn't dark enough use a darker stain. Then minwax stain is more of a dye stain than an oil stain so an actual wood conditioner would have been better than using mineral spirits. Last is the water based polyurethane. They are all incompatible with the linseed oil contained in the stain. The stain applied the way you did it should have been allowed to dry a week before using a waterborne finish. A shortcut you could have used is to seal the wood with a de-waxed shellac such as Zinsser Sealcoat before using the waterborne finish.

From where you are the only fix is to chemically strip the finish off, sand it and start over. Even if you decide to live with the light spots the finish will peal off.
 
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