Finds the commanding officer, executive officer and command master chief - known collectively as the leadership triad - all ashore together on a very dangerous mission. A Navy ship would never put the entire triad in harms way ashore at the same time.
El Toro's crew finds Chandler's radios, and reports that they are out of range. There would be no way for them to know this. A ham radio transmission is simply an outbound signal, there is no indication on the radio whether or not anyone received the transmission. It is unlikely that they would have tried using them anyway, as a transmission from a Nicaraguan rebel on the Navy radio would have alerted the Nathan James to trouble.
A ship's radar will not see past solid objects, yet the Nathan James is able to track the small boats while they're navigating the meandering river, surrounded by hills and mountains.
Edit: The Nathan James isn't using radar to track the location of the boats. The boats have transponders that the ship uses to track their location, crew members also often wear these transponders when on missions too, like when they were at Gitmo, the ship tracked their location using them.
Edit: The Nathan James isn't using radar to track the location of the boats. The boats have transponders that the ship uses to track their location, crew members also often wear these transponders when on missions too, like when they were at Gitmo, the ship tracked their location using them.
Near the nature reserve, the Nathan James listens in on the small boats' radio messages but maintains radio silence as to not disclose their location, yet keeps her ship's radar powered up to track those same boats. Furthermore, considering the small boats clearly came from the coast for anyone observing either the boats themselves or the radio status messages, it would be a simple conclusion that there is a larger ship at the mouth of the river.
When Chandler meets El Toro he introduces himself as just "Tom Chandler", he doesn't state his rank or position, nor is he wearing any visible rank insignia, yet El Toro addresses him as "Commander Chandler". It's obvious that Chandler is the commanding officer, so it would have made sense if he addressed Chandler as "captain" but the average person doesn't know that the CO of a destroyer is a commander, especially someone that isn't American.