The admiral says that Webb died in an explosion aboard a Japanese freighter "in the Baltimore shipyards". A shipyard is an industrial facility for building or repairing ships, not loading or unloading them. The ship is not at a shipyard (not in Baltimore and not anywhere else); instead it's moored alongside a pier on the waterfront in Baltimore.
Another common TV and movie mistake regarding the CIA is showing them conducting operations on US soil, investigating crimes and arresting people. The Central Intelligence Agency is a foreign intelligence service whose purpose is "gathering, processing, and analyzing national security information from around the world". They are not law enforcement and it is illegal for them to conduct operations on US soil as that is not their jurisdiction. Domestic intelligence gathering is under the jurisdiction of the National Security Agency (NSA). The CIA also has no law enforcement authority, CIA officers cannot arrest people or investigate crimes, if they uncover evidence of a criminal act they pass that information onto the proper federal law enforcement agency for further investigation, which is typically either the FBI or Homeland Security.
Employees of the CIA are not called "agents", it is a very common TV and movie mistake to refer to them as "agent" or "secret agent", no such titles exist. Intelligence personnel in the CIA's National Clandestine Service are known as either "Operational Officers" for field operatives or "Case Officers" for support staff that work in Langley. So the proper way to address Webb would not be "Agent Webb", but instead "Officer Webb".
Considering how many times Rabb has had someone try to kill him, in his own home no less, it seems out of character for him to not keep the magazine for his sidearm loaded at all times.