Or just buy more brass, the local indoor ranges here sell it for $50-$80 per 1000 pieces, I just throw out any 9mm or 45 auto brass that shows any problems. It's so cheap it's not worth putting any extra work into.
To dispose of the loose ones I would hand feed them so you know they won't get pushed back and let the brass be lost in the grass (or garbage can).
Just my opinion YMMV
The problem is finding these cases before they are loaded, and I know of no method of finding them. The case is tapered and the mouth of the case is .010 smaller in diameter than its base. You size the case then expand and bell the case mouth and taper crimp. This work hardeneds the case area that grips the bullet and the brass springs back more after sizing. The way to compensate for the brass spring back is to size the case slightly smaller. And on a rifle case they anneal the shoulder and neck area to make the brass softer again but this is not done on pistol cases.
I do not have this problem with .357 magnum or .40 S&W cases because they have little to no taper. But the 9mm is noted for this brass spring back problem especially with thinner cases.
I buy bulk once fired military Winchester 9mm brass that is thinner and size them with a under size Lee die. And this saves any problem with bullet grip and loose bullets.
You are correct the brass is cheap and to trash the bad cases, "BUT" you don't find the loose bullets until they are loaded. And the undersized die prevents this and extends you case life.
The Lee under size die only sizes the case .002 to .003 smaller in diameter to compensate for brass spring back and still have enough bullet grip. And if you have good eyes you "might" see the case is a smidgen more wasp waisted and has more than enough bullet grip.
Bottom line, resizing dies have a plus and minus manufacturing tolerances and its your "fat" die and skinny brass that causes the problem.
Look at the charts below, there is .004 difference in neck diameter between brands of resizing dies after sizing. And the 9mm loose bullet problem can be caused by the die or the expander. And the Lee under size die simply ensures proper bullet grip after expanding the case.
Are Your Sizing Dies Overworking Your Rifle Brass?
http://www.massreloading.com/dies_overworking_brass.html
Quick Tip: Undersized Resizing Die - Reloading
EGW Undersize Reloading Die, 9mm Luger (modified Lee undersized die)
http://www.egwguns.com/smithing-tooling/undersize-reloading-die-9mm-luger/
A must for the serious reloader: EGW offers custom designed, carbide sizing dies that are 0.003" smaller in diameter than typical dies. Not only is it smaller in diameter, but the bottom corner is also radiused which sizes the case further down. This helps prevent feed failures from cases that bulged near the base during reloading- which is typical of brass fired in Glocks and other loose chambered guns.