On their way to the submarine, Todd ask Gibbs "How do we get to the sub from the Frigate? Swim?"
Gibbs and Todd's helicopter is then seen landing them on the flight deck of a Burke-class Destroyer.
However, the next scene shows them in a whaleboat, leaving a Perry-class Frigate.
During one scene aboard the submarine, a sonar technician reports a contact on a certain bearing and at a certain "distance"; however, in the real world of the US Navy, the distance to a contact is consistently known instead as the "range", not the "distance".
When firing the water shot, the COB orders the outer door of the torpedo tube opened, then the tube flooded. The reverse order is the correct - when the outer door is open, the tube will of course flood on its own.
During one scene while operating submerged, the conning officer gives the order "250 feet", and shortly afterward the chief of the watch gives the report "250 feet and passing". The order "250 feet" requires the chief of the watch to reach the depth of 250 feet and maintain it, not pass that depth and continue going.
McGee identifies the blue cable as a DSL (Digital Subscriber Line) when it is just a standard Cat 5 cable. DSL doesn't require special cables, a standard phone line is all that is needed to connect the wall jack to the DSL modem. The Cat 5 cable is used to connect the modem to the computer and would then be called an EtherNet cable.
The time on the EAM (emergency action message) the sub received immediately after surfacing was 2302 (11:02 p.m.). The sub however had just been shown surfacing in bright daylight. However, when in action, military units switch to "Zulu Time" (UTC/GMT) to avoid confusion between command and/or field units which may be in different time zones.
When the crewman brings ice cream to Gibbs and Todd, he mentions Rocky Road ice cream and chocolate. Only one ice cream was chocolate colored and that was Rocky Road because of the marshmallows you see in it. There was no plain chocolate ice cream.