Some Catholic Popes who were famously arrested are Leo V, John X, Boniface VIII, Pius VI, Pius VII and Pius XII. Though there were several Popes who were arguably criminals, none of these arrests had to do with criminal behavior. Rather, the arrests were either retaliatory or an attempt to bend the Pope to the will of the arresting country or ruler.
In 903 during the Saeculum Obscurum, Leo V was raised to the Holy See but was deposed and arrested by the antipope Christopher. Christopher, in turn, was arrested and imprisoned by his successor Sergius III, and both Christopher and Leo V died or were murdered in 904. Pope John X was Sergius III's ally and later became pope himself. John X was arrested by Guy of Tuscany on behalf of the powerful Roman senatrix Marozia.
Boniface VIII declared that all spiritual and temporal power was held by the Pope, which exacerbated an existing conflict with King Philip IV of France. Philip and his minister Guillaume de Nogaret claimed Boniface was a heretic, so Boniface promptly excommunicated them both. In September 1303, Philip led an army against Boniface and arrested him, releasing him after three days. Boniface mysteriously died in October, allegedly of suicide from gnawing through his own arm and running headfirst into a wall.
In 1798, Pope Pius VI was arrested by French troops for denouncing the Revolution, and Napoleon also arrested his successor Pius VII in 1809. It has been alleged Pius XII was nearly arrested by Hitler in 1944 because Pius spoke out against German treatment of the Jews.