I have recently started using stains that are not oil based. Naturally they raise the grain. Yes I have tried wetting the wood surface and sanding before applying the stain but with less than desirable results.
Thinking about how I don't worry about dust and or the nibs that result when using a gel varnish, I knock all those down and smooth the final coat of varnish after it dries by rubbing a piece of paper, wrapped around a block of wood, over the surface.
I tried this with the fresh stained surface that was rather rough, smooth results.