When Sisko lists the people who would not have died if they had trusted each other, he mentions the runabout crew. However they were destroyed by the Jem'Hadar when they first arrived, before any contact had been made.
As O'Brien and Worf begin to fight, Sisko reminds them that they are both Starfleet officers. But O'Brien had JUST reminded Muñiz that he (O'Brien) was NOT an officer.
The Benzite that was piloting the doomed runabout was not wearing her portable gas emitter that Benzites use to breathe.
At the end of the episode, Worf joins Chief O'Brien in maintaining a vigil over Muñiz's casket, stating that it is Klingon tradition to "keep the predators away, until the spirit leaves the body". Once the Klingon Death Howl is made, Klingons regard the body "an empty shell", and pay it no more mind. This was more likely Worf's way of apologizing to Chief O'Brien for how tense things had gotten on the planet, and trying to mend their friendship.
When they are first exploring the downed ship, O'Brien runs into a dead Jem'Hadar hanging down. He fumblingly draws his phaser in reaction. Since they were exploring an enemy vessel, Miles should have had his weapon out beforehand.