Little ones should not really stink (but their brooder might). Are they getting covered with poo? If that is the case, and if you are also using shavings, you might turn the shavings with a cat litter scoop every day, and change it out completely every 4-5 days or per week if it really needs it. How many do you have in what size brooder?
And . . . the only other thing I can think of that might stink besides poo would be an infection of some sort. If you hold one up near you and take a sniff of its face/beak and it smells bad - - like infection - - then you might have a more serious problem. I am not seeing any folks with this issue on very young chicks, though.
Chicks are so RUDE! They don't bother to walk around another peep in the brooder...no, they just step on top of her. And they poop on each other...that's when I take one out and bathe her. Poor peeps - having to live with other rude peeps.