The letter from the Holy Office in 1949 to the Archbishop of Boston (here) clearly states,
The circumstances surrounding the excommunication were printed in an article in "The Catholic Advance" on February 27, 1953, which can be seen here. Pope Pius XII made three separate requests for Father Feeney to come to Rome. Clearly this meeting was to be about Father Feeney's denial of a Catholic doctrine, but when he did not show for the hearing, this was the final straw.
The "letter" so called was a political favor called for by Cushing because Feeney and others were exposing the heretical activities and teaching at Boston College and because Father Feeney was making converts at Harvard that were controversial.
Although the "straw that broke the camel's back" his public preaching against the Jews who Cushing went to great lengths to please and cater to.
He was embarrassed by these events and put the call in to his friends in Rome to have Father Feeney censured. He had influence among the Modernists and it was done.