Humans are also not perfect at fretting with the exact same pressure every time, or without inducing some bend in the strings. This is really noticeable with the G string which always sounds out of tune while playing, because our tuning system gives it a half-step-down intonation as a trade-off to make it easier to form chords.

James Taylor compensates by tuning everything down a few cents, between -12 at the low E and -3 at the high E, with a little break in the pattern with -4 cents at the G to deal with its weirdness. Good electronic tuners have "sweetened" presets which do something similar.