How exactly did Flint kill fifteen men with two (muzzle-loaded) flintlock pistols?
- Probably took a few out with the pistol shots (they'd go through the initial target at that range) then cut the rest down with his cutlass. They were all exhausted from hauling the treasure and digging the holes so there wouldn't be much of a fight.
- He obviously didn't kill all of them with those two shots; that was just the start of the massacre. The scene cuts away there because it makes for a dramatic ending to the song (BOOM!), and this way the audience immediately gets what's happened without having to drag the pacing down (and the rating up) by showing exactly how every single one of the fifteen pirates died. The important part is that he killed them all, not how he did it.
- Also, Billy Bones is an Unreliable Narrator — and not just because he's probably drunk during the telling of the story.
What happened to Big Fat Ugly Bug-Faced Baby-Eating O'Brien? She/he/whatever was never seen or mentioned after Role Call.
- She probably died at sea, or may have even been thrown overboard. It's bad luck to have a woman on board, after all.