qualms

1. A sudden feeling of sickness, faintness, or nausea.

2. A sudden disturbing feeling: qualms of homesickness.

3. An uneasy feeling about the propriety or rightness of a course of action.

Synonyms: These nouns denote a feeling of uncertainty about the fitness or correctness of an action. Qualm is a disturbing feeling of uneasiness and self-doubt: "an ignorant ruffianly gaucho, who . . . would . . . fight, steal, and do other naughty things without a qualm" (W.H. Hudson).
Scruple is an uneasy feeling arising from conscience or principle about a course of action: "My father's old-fashioned notions boggled a little at first to this arrangement . . . but his scruples were in the end overruled" (John Galt).
Compunction implies a prick or twinge of conscience aroused by wrongdoing or the prospect of wrongdoing: stole the money without compunction.
Misgiving suggests often sudden apprehension: had misgivings about quitting his job.