The council gave Long John Silver the black spot instead of Jim.
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The council felt that he'd made a mess of things, and that they'd all pay for Silver's mistakes.
From the text:
First, you've made a hash of this cruise--you'll be a bold man to say no to that. Second, you let the enemy out o' this here trap for nothing. Why did they want out? I dunno, but it's pretty plain they wanted it. Third, you wouldn't let us go at them upon the march. Oh, we see through you, John Silver; you want to play booty, that's what's wrong with you. And then, fourth, there's this here boy."
"Is that all?" asked Silver quietly.
"Enough, too," retorted George. "We'll all swing and sun-dry for your bungling."