c. 1600, "feeling of mistrust or sudden apprehension, a failing of confidence," verbal noun from misgive "make apprehensive, cause to feel doubt" (1510s), usually said of one's heart or mind, from mis- (1) "badly, wrongly" + give (v.) in its secondary Middle English sense of "suggest." Related: Misgivings.
"moral misgiving, pang of conscience," late 14c., scrupul, from Old French scrupule (14c.), from Latin scrupulus "uneasiness, anxiety, pricking of conscience," also, literally, "small sharp stone," a diminutive of scrupus "sharp stone or pebble," used figuratively by Cicero for a cause of uneasiness or anxiety, a word of unknown etymology.
Probably the notion in the image is of a pebble in one's shoe. The word in the classical Latin sense of "smallest unit of weight or measurement" also is attested in English from late 14c., and was given various extensions: "one minute of arc, one minute of an hour," etc. The Latin words commonly are regarded as identical, with sense development of the latter from "small pebble" to "small weight."