Character mistake: When Cutter is talking with Chief Biggs for the first time, right after the negotiations for fuel, Cutter says he is the former head of security for the airline. Since he has just been hired for that role (after being an independent security consultant), he should have called himself the future head of security, or new, or something of that nature. Former would indicate he has resigned from the position.
Continuity mistake: After the main bad guy gets back into the plane, he goes to the cockpit and tells the pilot to take off. Look out of the window. The sun is obviously setting, then overhead in the very next shot under the plane. This whole sequence up to the point where the plane is in the air again features changing times of day.
Answer: I just rewatched it this morning. When Rane is trying to persuade Sheriff Biggs that he means business, one body (presumably The Captain) is thrown out of the plane. Just before the passengers are released, we see a quick shot of yo ambulances. One has 3 full occupied body bags in it. Therefore, it's implied the other two are in the other ambulance. This takes place before the FBI guy gets there. The fact that he tells Rane, those guys you killed were my friends" means that at some point they were identified by name. He could've found out numerous ways (Washington told him, briefing, the paramedics, Biggs, etc).