A qualm is a feeling of uneasiness, or a sense that something you're doing is wrong, and it sounds almost like how it makes your stomach feel. If you had qualms about taking candy from the bulk bins at the store, your conscience probably told you to go back to the cashier and pay.
Qualm entered English in the 16th century, with meanings like "doubt" and "uneasiness." Usually a qualm comes from doubt about an action and a feeling that you are doing, or are about to do, something wrong. It isn’t a bad feeling about another person's behavior but about your own. If you have qualms about lying to get into the over-18 dance club, you might decide to follow your gut-check and meet your friends for coffee instead.