Sand them ALL lightly with coarser sandpaper (100-150) or a medium grade sanding sponge, going with the grain, and apply a second coat of stain to ALL of them.

Then evaluate the results.

If you try to fix part of them they never seem to get in synch with the ones you like.

Do not try conditioner again. It has done it's job [sort of] and you can't go back.
Lazyg has the idea that will get you started on a fix. Beware that the result will be dark, maybe darker than you wanted.

Minwax prestain conditioner stinks. I'll never use it again; I got exactly the results you did.

After a lot of desperate research, I tried a washcoat of 1 part zinsser bulls eye seal coat dewaxed shellac mixed with 2 parts denatured alcohol. Brush on thinly and evenly, try not to overlap, maintain a wet edge (but I've never seen my overlaps, still, it's good wood finishing practice.) It was a nuisance to buy and mix up the stuff, but it's a dream to work with, and the results are absolutely worth it. People will think you're a god(dess) of wood finishing when they see the results.

After the washcoat, apply your stain (I prefer gel) and your topcoat such as polyurethane, varnish, etc.

Also, the alcohol and shellac are very fumey, but non-toxic and quick drying, so you dont have to worry about dust accumulation. It's great stuff. I joke to my husband that if I mixed shellac with vodka instead of denatured alcohol, I could sip it while I work.

The other thing is, you might want to quit buying minwax stuff and switch to general finishes. Harder to find but worth it. Their gelcoat wiping varnish is so much better to work with than the minwax polyurethanes. But the minwax gel stains aren't too bad.

Here is a link that might be useful: what the heck is a washcoat anyway?

It's very difficult to get an even stain on some hardwoods like beech and birch. Floor manufacturer's recommend that you go with the natural color.

You may be able to go with a colored top coat varnish.