Doc Rios confronts Quincy when he is below decks ready to pull the safetied Halon discharge pin and says that doing so would "flood the whole engineering room with poisonous Halon gas". Halon gas is extremely non-toxic, breathable, and one can inhale it without any adverse effects. It is so safe that it is used to fight fires in enclosed spaces such as aircraft cockpits, and there is not even a need to don oxygen masks in the cockpit before it is discharged. On the other hand, CO2 extinguishers, which displace so much oxygen that a human would pass out if it were to be discharged in an enclosed space, would require an oxygen mask to be donned before it was used. Doc Rios would be well aware of these facts.
The two lieutenants steer their armed small boat to the Russian ship, abandon same fifty yards before it slams into the ship. the USN Last Ship having cleared the coral field then announces all they have to do is pick 'em up which they do, however the Last Ship was nowhere near them.
The helicopter that took off to investigate was a Seahawk with FLIR in the nose. Then we see a Blackhawk passing by. Blackhawks have their tail wheel at their tail while sea-hawks have it in the middle.
If the disease is airborne and that virulent the soldiers should be in full NBC gear anywhere on the island as a matter of protocol. The virologist should have informed them of that. Also, any item or equipment should have been disinfected before being brought on the ship.