Continuity mistake: Just as the F-14's are coming under fire from the ship, we are shown the pilots. One of the pilots, "Pendry" was killed when his F-14 crashed due to a malfunction in the earlier episode 'Pilot Error'. As such, "Pendry" could not have been fired on in this episode since he was already deceased.
Factual error: Throughout the series the captains of ships are generally portrayed as holding the rank of captain, regardless of the class and size of the ship they command. In reality the rank of the CO of a frigate would most likely be a Lt.Cmdr or Cmdr whereas the CO of a amphibious ship or a carrier would be a Captain. On these larger ships the XO usually holds the same rank as the CO, but obeys all orders given by him. However unlike in JAG the CAG takes most orders from the carrier group commander (2 star), not the CO.