How to fix a finishing defect?

I am finishing a cabinet with a water based dye and then a gel coat. I used filler on some joints. The area was not big, so I didn't think it would be a problem. In the past my experience was that filler sucks up stain and get dark, but just the opposite happened here. The filler seemed to shed the stain and is now lighter than the rest. It is the first time I have used dye or gel stain; is one of them the problem?
Anyhow, I would like to touch up the problem. Any suggestions how? I haven't varnished yet, but I expect there is some varnish in the gel stain.
Thanks
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Seal with dewaxed shellac. Color with medium of your choice. I like acrylics. Seal again with dewaxed shellac. Topcoat as desired.
Good Luck.

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