Fenwick's episcopate involved numerous conflicts both among parishioners over control of their respective churches, and between parishioners and the bishop.
Some of these disputes turned violent, and involved calls for leaving the Catholic Church to create new churches.

One such dispute arose at St. Mary's Church in the North End of Boston in 1840.
That year, Patrick O'Beirne and Thomas J. O'Flaherty were appointed co-pastors of the predominantly Irish church.
The parish quickly became polarized, with parishioners supporting either O'Flaherty, who advocated strong lay control of the church, or O'Beirne, who advocated episcopal control.
Divisions were further deepened by O'Flaherty's support of the temperance movement and opposition to the Acts of Union 1800, which united Ireland and Great Britain.
By 1842, the congregation was so divided that Fenwick worried violence might erupt.
Therefore, he attempted to restore peace by personally visiting the church, threatening excommunication for disobedience of church authorities, banning mass protests, and ordering the two pastors to publicly reconcile.
Eventually, Fenwick transferred O'Beirne to Providence, Rhode Island, at O'Beirne's request.

None of these efforts were effective in restoring tranquility, and on February 20, 1842, O'Beirne's supporters began a riot during a Vespers service over which O'Flaherty presided.
The perpetrators were arrested and prosecuted, and Fenwick placed the parish under interdict for two weeks.
He then transferred O'Flaherty to Salem, Massachusetts, and removed O'Beirne from Providence.
Though O'Flaherty's supporters demand his return, and organized regular train rides to visit him, the dispute at St. Mary's came to an end.
Fenwick's episcopate involved numerous conflicts both among parishioners over control of their respective churches, and between parishioners and the bishop. Some of these disputes turned violent, and involved calls for leaving the Catholic Church to create new churches.
One such dispute arose at St. Mary's Church in the North End of Boston in 1840. That year, Patrick O'Beirne and Thomas J. O'Flaherty were appointed co-pastors of the predominantly Irish church. The parish quickly became polarized, with parishioners supporting either O'Flaherty, who advocated strong lay control of the church, or O'Beirne, who advocated episcopal control. Divisions were further deepened by O'Flaherty's support of the temperance movement and opposition to the Acts of Union 1800, which united Ireland and Great Britain. By 1842, the congregation was so divided that Fenwick worried violence might erupt. Therefore, he attempted to restore peace by personally visiting the church, threatening excommunication for disobedience of church authorities, banning mass protests, and ordering the two pastors to publicly reconcile. Eventually, Fenwick transferred O'Beirne to Providence, Rhode Island, at O'Beirne's request.
None of these efforts were effective in restoring tranquility, and on February 20, 1842, O'Beirne's supporters began a riot during a Vespers service over which O'Flaherty presided. The perpetrators were arrested and prosecuted, and Fenwick placed the parish under interdict for two weeks. He then transferred O'Flaherty to Salem, Massachusetts, and removed O'Beirne from Providence. Though O'Flaherty's supporters demand his return, and organized regular train rides to visit him, the dispute at St. Mary's came to an end.
Benedict Joseph Fenwick