Franks said that the Naval Investigative Service (NIS) became the Naval Criminal Investigative Service (NCIS) in 1992. However NIS was restructured into NCIS during the later months of 1993, with NCIS's official founding taking place on December 14, 1993.
The Military Sealift Command does routinely contract privately owned cargo ships and crews like the Cape Fear to transport cargo, vehicles, medical supplies and sometimes even small arms like grenades, pistols, rifles, machine guns and their ammo. However when it comes to transporting large explosive ordinance like bombs, guided missiles, torpedoes or any other kind of weapons system whose designs are classified are transported on Navy-owned ships crewed directly by Sealift sailors and Merchant Marines; they are not private contractors but federal government employees who must be U.S. citizens and pass a very thorough background check. The bomb that Pula is shown sabotaging appears to be a GBU-30 series laser guided precision bomb (warhead yield equal to 1,200 lbs of TNT), which are carried on fighters like the F-15E Strike Eagle, F-16 Falcon, F/A-18 Hornet, F-22 Raptor, F-35 Lightning and strategic bombers like the B-1B Lancer, B-2A Spirit & B-52H Stratofortress; munitions like this or a Tomahawk cruise missile are only transported on Sealift ships like Lewis and Clark-class dry cargo/ammunition resupply ships, never private contractors due to security issues.
Deputy Director Welsh is likely supposed to be the deputy director of the NSA, his title on the MTAC screen says NSO but there is not such organization, so it is likely a typo; he appears to be heading the intelligence side of this operation, so him being NSA makes the most sense. He disagrees with Gibbs' conclusions and says he will not order the frigate to break off from the Cape Fear, however he has no authority whatsoever over military operations; in fact none of the civilian intelligence agencies do, so it ultimately doesn't matter what agency he is supposed to be with. However Captain Tom Zill, a Navy officer who is the deputy commander of Sealift Logistics Command (SEALOGLANT) that is also on screen, agrees with Gibbs and he would have authority over what happens to the Cape Fear as it is a Sealift Command vessel; acting under the authority of the commanding officer of SEALOGLANT, who is a one-star Rear Admiral, he would have the authority to order the frigate to stand down.
The frigate intercepting the Cape Fear has the hull number FFG-19, identifying it as the USS John A. Moore, a Oliver Hazard Perry-class guided missile frigate. The USS John A. Moore was decommissioned from the US Navy in 2000, six years before this episode takes place. It was technically in service in 2006 but not with the U.S. Navy, it was sold to the Turkish Navy in 2001 so it wouldn't have been part of a U.S. Navy operation in 2006.
NCIS has the Military Sealift Command send out wanted posters for Pinpin Pula to all of their vessels, as a general fax message, warning them of his true identity & intentions and ordering ship's security to place him under arrest if spotted. However NCIS knows from interrogating the Turkish freighter captain, and from the ship's crew roster, that Pula is a radio operator; making it logical to deduce he is likely also working as the radio operator on the Sealift vessel he infiltrated. Which would put him in the perfect position to intercept any general messages like faxes. Instead the BOLO information for him should have been relayed directly to each ship's master (captain). Like the Navy, the Sealift Command has protocols for sending encrypted "eyes only" messages to the commanding officer of a vessel; knowing this information, and considering the danger to the lives of the thousands of sailors and Marines in the Amphibious Strike Group, if Pula's mission is carried out the warning about him would be sent directly to the master of the vessel.
When Jenny Shepard trying find somebody who help Gibbs to remember after DesertStorm (including his Marine unit in Desert Storm and his former mentor in NCIS) and after discovering about his hidden deceased family, somehow she forgot about checking up on his father Jackson Gibbs (who was later in future episode "Heartland" revealed very alive) to informed him that his son was seriously injured and he was in a coma.
It is revealed that Gibbs joined NIS in August of 1991 following the death of his wife and daughter. However, in the JAG episode "Ice Queen" in 2003 he tells Lt.Cmdr. Rabb that he has been an agent for 19 years, which would mean he would have joined NIS in 1984.
Dr. Gelfand says that Gibbs is suffering from "disassociation". The correct psychiatric term is "dissociation".
While revealing Gibbs's first marriage and daughter to Ducky, Jenny Shepard says Kelly (Gibbs's daughter) was born in '84, and died as an 8-year-old while Gibbs was fighting in Desert Storm. Fighting or 'Major Combat Operations' of Operation Desert Storm (or Desert Shield) ceased in early 1991. This makes it impossible for Kelly to have been 8 years old at the time of her death.
Kelly was born in '84 and killed in '91, which would make her 7 years old, yet Shepard said she was 8 when she was killed.