Are you sure that grain is dead flat? Perhaps the absorption of finish has created some tiny bit of uneven swelling. I have seen that happen with knots (which don't swell and thus become depressions occasionally).

I would be tempted to run a hard flat block of very fine grit paper across that area, recognizing that it may set you back on the finishing process.

Also, the butt pad seems to be pulled away from the wood slightly. Was that there originally, or is that really something else and just a photo illusion?

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BrentD, (Professor - just for Stan)
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[Linked Image from i.imgur.com]