The submarine that breeches magically transforms into a different boat when it gets underway.
At the end of the episode, when the COD is launched, Harm and Kate are thrown back into there seats from the acceleration. Since the seating in the COD faces the rear, they should have been thrown forward from their seats.
Harm pilots the F-14 Tomcat to safety since the CAG as pilot is injured. The Radar Intercept Officer in a F-14 does not have flight controls thus it would be impossible to pilot the Tomcat. They should have ejected instead.
The ATARS system that the CAG is using to take recon images of the Bosnian mobile missile launchers is only used by the variant of the F/A-18D Hornet flown by the United States Marine Corps, it is not used by the U.S. Navy F-14 Tomcat being flown by the CAG.