Which issue did catholics and protestants disagree about that led to their radically different art?

The protestants did not believe in worshipping saints, because they believed that the Bible should be the only word that is respected in Christianity. There is evidence of this in art, as many Catholic art represents saints being worshipped, while you will not find any saints in Protestant art. Rather, most Protestant art is depicting stories directly from the Bible.

There were many issues that the protestants and Catholics disagreed about.
Catholic art responded to the reformation by depicting the issues that were being challenged. So in Catholic art you will find the virgin Mary or art depicting the dogma of the immaculate conception or saints eg Saint Catherine being welcomed into heaven. In general Protestant art tended to avoid: grandiose images of Jesus or the Virgin Mary; big set-piece scenes from the Bible (like the Passion of Christ); images of the Saints; and, in particular, depictions of the Popes and other senior clergy. Instead, Protestant art focused on humble depictions of biblical scenes and moralistic depictions of contemporary everyday life. Also the division of the sacred and the secular.