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.
She was obviously intended as a one off gag, but the above ideas are possible as is the idea that she was still on board, just offscreen.
How come the movie ends with Long John losing the treasure and being stranded on Treasure Island? You can bring up nobody at Disney wanting Long John to get a Karma Houdini, but Mr. Arrow lives unlike in Stevenson's novel.
The lifeboat that he took was unsafe, and he couldn't have taken the heavy gold with him when he abandoned the lifeboat. And as for why the lifeboat just happened to be unsafe, I'd call it his karma for trying (even though unsuccessfully) to kill Mr. Arrow by stoking his fear of unsafe lifeboats.
Blind Pew would have known Billy Bones was going to try to make a run for it when he got the Black Spot, so why didn't Pew come with the gang of pirates in the first place to try to stop Billy?
Why, if Captain Smollet served with Jim's father, does he ask which one is Hawkins? Shouldn't he know that the human father had a human child?
Well, in The Muppets, the very Muppety Walter and the very human Gary are brothers and nobody questions that. And in The Great Muppet Caper, Kermit and Fozzie play "identical twin brothers" and though the fact that they don't look anything alike is mentioned, nobody questions how a frog and a bear could be twins. In the Muppet world, it's apparently perfectly possible to have blood relatives that are not the same species. We don't even know if Jim's father was human! So, Smollet probably figured it was best to ask.
Also a big part of the joke is probably that Muppets don't really see race/species unless it's relevant to the current gag.