I have been the pissed off employee and I also own my own business and hopefully don't have pissed off employees lol. Seriously though just take the discount the last thing the employee or the employer wants is to discuss a discount. Trust me as an employer we don't care about discounted items. The markup is way to high for us to care. As the pissed off employee I am probably going to quit the job soon anyway so don't put much thought into the discount. The employees know the markups and how the system works just as well as the employer.

At Target: Tell her to take more.
At Liquor store: Help him to his car with them.
At Department store: Wouldn't charge you at all.

Oddly enough, that just happened to me. I was in Petco and saw a dog toy I knew my Malti-Poo, Cyrus King of Persia, would love. It had a clearance tag on it. When I went to check out, it couldn't scan, so the lady just charged me a dollar; it was store policy for clearance stuff that got separated from price tags.
Cyrus loves his new giant mouse.

But on the contrapositive of this issue, if something has a price and the checkout person charges too little, I always correct it.