At the very end of the movie, when the U.S.S. Stingray is tied up to the pier and the crew is marching off, a white-hulled vessel is visible in the background. This vessel is a 95 foot retired Cape-class U.S. Coast Guard Cutter (U.S.C.G.C. Cape Romain), which was at the time operated by Sea Scout Ship 17 (youth program similar to Boy Scouts), based out of San Mateo, CA. The ship was requested to be on-location at a pier in San Francisco (most of the harbor footage was shot in the Bay Area; the mothball fleet depicted early in the movie really exists and is near Benicia, CA) to make it appear more like a military base. The Cape Romain is currently operated by Sea Scout Ship 51 (S.S.S. Intrepid), based out of Palo Alto, CA.
In the scene towards the end where Lt. Lake enters LC Dodge's cabin and kisses him, Lauren Holly hits her elbow backing out the doorway. This was unintentional and Kelsey Grammer's reaction almost ruined the take. As a noticeable bruise developed during later takes and they (Grammer and Holly) couldn't stop laughing, this was the take used.
Dodge objects to Lt. Lake's assignment to the Stingray, citing the U.S. Navy's rule against women on board submarines. The film was released in 1996, one year after Norway became the first naval power to promote a female officer to command of a submarine.
While it has been criticized for some of its concepts, many of the underlying ideas of the movie are accurate. Modern diesel submarines (not a retired World War II submarine) using their electric batteries are capable of being notably quieter than nuclear submarines. Many navies operate modern versions of the submarine shown, and their vessels are quite effective in their roles. Experts have criticized the U.S. Navy at various times for not employing a few of this type of submarine in the force.
When Dodge and the Admiral are talking just after he's seen the Stingray Dodge asks if he's supposed to turn the submarine into a museum. The 'Pampanito', the sub used in the movie, is a museum at pier 45 in San Francisco.
At the end of the movie, Lt. Cmdr. Tom Dodge ('Kelsey Grammar') is informed by Vice Adm. Dean Winslow (Rip Torn) that he would not be receiving a Los Angeles Class submarine, but would instead be placed in command of a Seawolf Class submarine. The Seawolf Class was intended to be the replacement for the Los Angeles Class, however due to high costs, only three were ever built. Ultimately the more cost-effective Virginia Class was chosen to succeed the Los Angeles Class in the US Navy.
The trivia item below may give away important plot points.
When the crew takes the 'Stingray' on its test dive after renovating the boat, Commander Dodge orders a depth of 500 feet. On the way down, as they pass 400 feet, Lieutenant Lake remarks that this was "crush depth". 400 feet was, in fact, "test depth" rating for the 'Balao'-class submarines. Meaning the submarine was not to be dived any deeper than 400 feet during peacetime, and is approximately 2/3rds of the depth the submarine was designed for. It might also be noted that there are several reported and accepted instances during WWII in which submarines went below their "crush depth" for short periods and survived relatively unscathed.