What horrible offense does Dick commit that leads Silver to tell him to pray?

Dick gave Silver the black spot. The paper he used to make the spot was taken from the Bible.

"Step up, lad," cried Silver. "I won't eat you. Hand it over, lubber. I know the rules, I do; I won't hurt a depytation."

Thus encouraged, the buccaneer stepped forth more briskly, and having passed something to Silver, from hand to hand, slipped yet more smartly back again to his companions.

The sea-cook looked at what had been given him.

"The black spot! I thought so," he observed. "Where might you have got the paper? Why, hillo! Look here, now; this ain't lucky! You've gone and cut this out of a Bible. What fool's cut a Bible?"

"Ah, there!" said Morgan. "There! Wot did I say? No good'll come o' that, I said."

"Well, you've about fixed it now, among you," continued Silver. "You'll all swing now, I reckon. What soft-headed lubber had a Bible?"

"It was Dick," said one.

"Dick, was it? Then Dick can get to prayers," said Silver.