The statement that a minhag trumps halacha is a bit misleading. Where there are multiple legitimate halachic positions and there is a minhag comports with one of them, we will follow the minhag, even if the majority position is against the minhag.
In other words, a minhag without any halachic support is a minhag shtus or minhag taus. A minhag with halachic support, however, can override the normal klalei horaah and the halacha would follow the minhag.