In the beginning of the movie, Ed Harris breaks into the holding site for the rockets. When he is in the room, he asks for 16 rockets. After Goodspeed and Mason go into the morgue, he de-bombs 12 rockets. Mason then tells him he needs to find three more rockets, and he does. But that would not add up right. 12+3=15. He originally got 16.
When they broke into the base, Ed Harris asked for 16 rockets, but remember that one guy dropped one and had to be sealed inside. They only got 15 rockets out of the base.
If you watch the beginning again you will see that the last rocket is dropped and the chemical is released before they can get a replacement for the rocket dropped...
Hummel originally asks for 16 rockets but he only walks-out of the hangar with 15. Your missing rocket is the one that accidentally fell apart and killed the soldier while he was carrying it out. Hummel then has to lock him in with the other rockets to prevent contamination.
When General Hummel walked into the storage room for the Gas, he turns around and says "I want 16 Major". Later in that scene one of the marines slips while grabbing one of the containers dropping it. Major Baxter evacuates everyone sealing in one marine escaping the facility with only 15 containers.
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