It's a battle, all the way. Any spirit stain is essentially solvent with color. Over enthusiastic staining - rubbing too hard and/or too many coats - or sanding just a bit too deeply throught the finish will show pin holes in the filler. It is more difficult to fill all the pores in a stock that most folks imagine. These holes rarely show until the final finish is applied. Dull finishes don't show the pores as readily, with ANY shine they leap right out there at you.
Staining adds numerous complications and much work to any stock finishing. I have no sure cure, and a stock with pin holes showing in my drying cabinet. Do you live with a few pores showing, or not?
My best advice is to try to imagine where the problem occured, then repeat the step that didn't work.
I really don't mean to be a wiseass, but:
Did I mention, I've never been completely happy with any stock finish I've ever done? Every time I get a really good one, the next one is a [censored].
Did I mention that most stockers shy away from staining because of the added difficulties?
Did I mention that after thirty years I still struggle with processes that seem like I should have them down?
Two things in this shop that are never a given: Stock finishing and rust bluing. There are always variables in both processes, I do the best I know how, and if that doesn't work, try something else or do it again.
Sorry there is no pat answer, and I may not seem the expert you imagined.