You can think of niggle as something very small that keeps rubbing — a stone in your shoe rather than a blow. It is too small to stop you, and too constant to forget. Every use keeps both halves of that picture: the size is tiny, and it will not leave you alone. The stone can sit in your mind, in your mouth as a small complaint, or in your knee.
From the word’s history
Wiktionary records niggle from 1599, origin uncertain, likely borrowed from dialectal Norwegian nigla (to be stingy, to busy oneself with trifles), ultimately from Old Norse hnøggr (stingy), related to Old English hnēaw. If that route is right, the word has been handling small amounts from the start.
Wiktionary 說 niggle 1599 年就有紀錄，來源不確定，可能借自挪威方言 nigla（小氣、為瑣事忙來忙去），再往上連到古北歐語 hnøggr（吝嗇），跟古英語 hnēaw 同源。如果這條線成立，它從一開始碰的就是「小」——小氣、小事、小份量。這一點正好和今天的每個用法接得上。
Wiktionary etymology text supplied in packet (kaikki:3f6f69a190036ae4:621244510:3152 and :621247662:8293)
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