I was fired from a retail store in KY for making a price adjust incorrectly. My employer (big national chain) made me sign an agreement to pay them the difference in order to avoid prosecution for my mistake. They said if I didn't sign it, I would be led away in handcuffs. Since it was a mistake on my part, can I actually be prosecuted? (The customer it benefitted was a complete stranger.) Also, can they force me to repay them?

I don't know about the criminal aspect of this, but as far as your paycheck is concerned, they could not deduct the loss from your pay. See here:
http://www.kylabor.net/esat/wagehour.htm#h