Continuity: Various episodes - Harm and other pilots take off, fly and land in different aircraft during the same mission (understandable because of available footage).
Miscellaneous: The hull numbers on ships often do not match the ones displayed on the base caps etc. worn by the crews.
Factual errors: In later seasons of JAG, the introduction shows a brief segment of AH-64 Apache attack helicopters flying in formation. However, as the opening credits are intended to display Navy and Marine Corps activities, this would be a bit out of place, as neither the Navy nor the Marine Corps operates the AH-64 - in the US Military, only the Army does, while the Marine Corps employs the AH-1W 'Whiskey' Cobra.