My IPA WTF moment was when I learned that "t͡ʃ Voiceless palato-alveolar affricate" and "t͡ɕ Voiceless alveolo-palatal affricate" are two different sounds. The first is English ch (as in church), and the second is Korean ㅊ (or so they say), but even being a native Korean speaker, I just can't tell the difference.

(They do sound somewhat different but that's because English ch is always pronounced with rounded lips.)

Also, seriously, couldn't they think of a better name than "palato-alveolar" vs "alveolo-palatal"?