Hi,
Since minwax is extremely slow to fully dry, you can probably rub the imperfections out with a cloth. Don't be in too much of a hurry to apply another coat; unless fully cured, the previous coat will be partially dissolved by the next coat; net effect being not darker.
Sanding will take off more than just the imperfections. Some interesting timeworn/antique effects are achieved by sanding through the stain layer and exposing bare wood.
Casey

I think the worst case scenario is that you have a pigmented Minwax stain, and when you sand, you remove the pigment from the high parts of the surface and leave it in the low parts (pores), accentuating the contrast, then further, the first two coats of stain have sealed the high points and don't allow the "penetrating stain" to soak in and there's no where for the pigment to lodge. Worst case.

If it was up to me, I'd try a white Scotch Brite pad (finest), and rub in the next coat of stain. But I'd try it in an inconspicuous spot first, not dead center on the top.

Or...my real preference: I'm presuming if you're using Minwax stain, your probably going to use the ubiquitous Minwax Polyurethane. I thin the first two coats 50-50 with mineral spirits, then sand almost all of it off to be a self-sealer. That should take care of your bugs. Then sand again between each subsequent coat of finish.

Actually I'm going to be finishing with Behr Tung Oil Finish.

Could I get smoothness by just sanding after the first coat of finish and applying a 2nd coat? The surface isn't horribly rough now, just rougher than I would like.

A light sanding as you describe will do absolutely no damage, just sand straight with the grain. Sanding between topcoats will improve the finish. I use 280 stearated paper.

Wait....did you say Wet sand? No, unless you use mineral spirits. That won't add anything though and will wash off some of the stain, just scuff off the foreign material that is stuck in the stain.

Thanks for the advice everyone. I can always count on Gardenweb for help with my problems...

What I ended up doing was giving it a good hard rubdown with a tack cloth and that seemed to do the trick.

I'm in the same boat essentially. I have antique red oak and it's beautiful but there are places where I want to go back over and I'd like to just sand the whole thing, lightly, wet sand. None of the answers to your questions or issues helped me at all. I'm forging ahead with a damp 320. Good luck to you with your project.