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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Other: When Holmes and his gang are running from the Germans through the forest, one of Moriarity's German lackeys yells that it is time to introduce them to "Little Hansel" (in subtitles). Strangely, what he really yelled was, "zu viele Fuchse fur euch paar Huhner," or "too many foxes for those few chickens." Not sure why they made such a change in dialogue (where the German phrase was ever thought to fit in).
Factual error: In the scene where Holmes enters the factory in Germany, a map can be seen on a table with small German black-red-gold tricolor flags sticking up from it. However, the flag of the 2nd German Empire at the time of the film's setting (1891) was black, white, and red, and was so from 1871-1918.
Factual error: In the scene where Renč was dying, Dr. Watson examines the dying man and the poisonous arrow that hit him, and concludes that the venom used was curare. Curare is a paralysing poison that causes the body to relax to the degree that respiratory muscles stop contracting and the victim dies of asphyxiation. René on the other hand perished in strong cramps and foaming of his mouth.
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.