Factual error: When Holmes and Watson climb back into the train carriage, Watson pulls the door shut with ease. As the train is going quite fast (50+ mph) and the door opens against the carriage it would be take a lot more effort to close, as he is pulling it against the wind the train is producing.
Continuity mistake: When they are running through the woods, the marksmen shoots one of the fleeing gypsies. The scene goes to slow-mo and we see the bullet goes through him and hits the tree behind him. When the scene switches to the women watching him fall, the tree behind him is unmarked.
Other mistake: In the scene when Sherlock Holmes and his crew are running through the forest, the barrel of "Little Hansel" can be seen being raised up to 50°, which would cause a parabolic trajectory, but the shell travels in a horizontal path as it blasts through a tree and past Holmes.
Continuity mistake: In the scene where Watson goes to the telegraph office and finds it is locked, he kicks the door in, visibly damaging the frame. But once he comes out the frame is fixed and the door is lockable.
Continuity mistake: The soldiers on the train that are set on fire simply disappear once the door is closed, including the fire.
Continuity mistake: Sherlock looks at the ring of a murdered man, who was killed in a blast along with about a dozen other men in Paris, and the ring was plain. But later, the ring is shown again, and this time it has the letter M on it, a large letter, and it is very ornate - nothing like the other ring.
Continuity mistake: In the ballroom scene of the peace conference, Sherlock is dancing with Madame Simsa in the close-up, when the shot goes to the wide shot of the dancing, the dancing Sherlock and Simsa are nowhere to be seen, instead Simsa can be seen in the lower left hand corner of the scene, talking to Watson.
Audio problem: In the beginning when Holmes "shoots" the dog, Gladstone, with a dart and Watson says "What have you done to Gladstone now?", look closely and Watson's mouth doesn't move.
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 Renè 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.
Continuity mistake: The first time Sherlock shows his camouflage suit, its brown colour changes between the first and second shot. The first one matches exactly that of the room, but the second doesn't. Clearly the first one was achieved with a green-chroma-suit, and the second angle was a coloured fabric.
Other mistake: 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).