Dr. John Watson: What are we doing down here?
Sherlock Holmes: *We* are waiting. *I* am smoking.
Toward the beginning of the film, Watson enters Holmes' room on Baker Street that's full of eccentricities; looking out the window is a mannequin to act as Holmes' doppelganger. This idea was first used in the short story "The Empty Room" found in "The Return of Sherlock Holmes". The dummy was used again in the short story "The Mazarin Stone" found in "The Case-Book of Sherlock Holmes". See more...
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Plot hole: Irene Adler died of a type of tuberculosis that was so lethal that she coughed up blood and died within minutes. Moriarty picks up the blood stained handkerchief and later gives it to Sherlock who is seen sniffing it sentimentally. This lethal variant doesn't seem to affect either of them.