'mis-set' is formed from the prefix 'mis-' (from Old English 'mis-' meaning 'wrongly, badly') + the verb 'set' (from Old English 'settan', meaning 'to cause to sit, put in place').

'set' comes from Old English 'settan'; through Middle English it became 'set' with the sense 'to put, place, fix', and the productive negative prefix 'mis-' was attached in Modern English to create 'mis-set'.

Originally 'set' meant 'to put or place'; with the prefix 'mis-' the compound's sense became 'to put or place wrongly', a straightforward negative/incorrective meaning that has persisted.