The law in many states prohibits a person from carrying a long gun in a vehicle unless the firearm and ammo are in separate compartments, one of which must be locked. I guess the subway car meets the definition of a vehicle -- at least according to the arresting LEO.
“In Pennsylvania a License To Carry Firearms is only required to conceal a firearm, or to carry a firearm in a motor vehicle. The law is silent on the act of openly carrying a firearm while not in a vehicle making it de-facto legal. It must be noted however that due to 18 Pa.C.S. § 6108 (Carrying firearms on public streets or public property in Philadelphia) a License To Carry Firearms is required to carry a firearm in any manner on the streets or public property of a “City of the first class” (Philadelphia.)”