It's possible that Hegseth and the Pentagon has threatened the Holy See, with what was not clear, but they called the Vatican's Ambassador to the United States to the Pentagon and made a formal complaint over the comments made by Pope Leo with respect to America's war with Iran:
http://www.mediaite.com/media/news/jd-vance-confronted-with-report-the-pentagon-allegedly-threatened-vatican-with-military-force/
It's been reported that the Pope may cancel a planned visit to the US as a result of this meeting, and could further forgo any visits while Trump remains in office.