What did the medieval Spanish have against the Jews? Religion and Otherness? In that Catholic world Jews were heretics, and they had customs and language that became foreign as Spain redefined itself as Christian only.
Jews no longer fit in New Christian Spain, and the Spanish reacted by expelling them.
Those who wanted to stay became a pariah class of people who were Spanish in language and culture but tainted by Jewishness.
Even converting to Catholicism could not cleanse the mark from them.