Workers discovered 900 bodies in unmarked graves along the Old Common Burial ground during construction. Other problems plagued the project. Nearby buildings were subject to occasional flooding. The pastor at Park Street Church called the subway an "infernal hole" and an "un-Christian outrage."

Six months before the first subway ran, a gas leak during construction and a streetcar spark on the rail caused an explosion that ripped through the Boylston and Tremont street intersection, killing 10 and injuring 50.