Between 2003 and 2005, "JAG" and NCIS (2003) had different Secretaries of the Navy, even though the two shows exist within the same universe.
In the intro, the narrator gives Rabb's rank as Lieutenant Commander when he crashed, and was diagnosed with night blindness, yet throughout the first season his rank was Lieutanant, and he was already in the Judge Advocate General Corps.
Various episodes - Harm and other pilots take off, fly and land in different aircraft during the same mission (understandable because of available footage).
Throughout the series ships' crews wore their covers, whether they be ball caps or dress covers, while aboard ship. Navy regulations require covers to be removed by all personnel while inside a ship or a building. On a carrier when out at sea, indoors or out, covers are removed. If a cover flew off on the flight deck it could damage the engine of an aircraft.
Every scene begins with a graphic which depicts the time in military format and the word "Zulu". Zulu is the military phonetic designation for the time zone known as Greenwich Mean Time (GMT) or Coordinated Universal Time (UTC). In most cases, the time listed corresponds to the apparent local time rather than ZULU time. For instance, a scene set in Norfolk, Virginia in which the characters are eating breakfast in the mess would be labeled "0700 ZULU", but is more likely 0700 Eastern Standard (Romeo) Time or 0700 Eastern Daylight (Quebec) Time and certainly not 0700 Zulu, which would correspond to a local time of 0200 or 0300, which would be early even by military standards.
The Judge Advocate General Corps of the US Navy is actually located at the Washington Navy Yard in Washington D.C.
In several episodes, the show's writers confuse the United States Penitentiary at Leavenworth and the United States Disciplinary Barracks at Fort Leavenworth. The USP is a federal prison. The USDB is the military prison. On several occasions pictures of the USP are used to represent the Disciplinary Barracks.
Throughout the series, when aboard ship, the baseball caps have a silhouette of the ship. The actual caps have only a blank space between the ship's name and hull number. This space is filled with a pin designating the person's rate/rank.
The hull numbers on ships often do not match the ones displayed on the base caps etc. worn by the crews.
Numerous times throughout the series, when the Pentagon is shown it's identified by the text as being in Washington D.C., though the technical location is Arlington in Virginia. However it has been insisted by many that it is highly linked to D.C.'s political and economic culture that the employees think of themselves more as 'Washingtonian' than 'Virginian'.