When Holmes, Watson and Freud are attacked by rampaging horses, the trainer can be seen running behind the horses in long shots.
During the railroad pursuit the sword fight atop of the carriages shifts indiscriminately from cut to cut between the roofs of the second and first coach.
During the railroad pursuit, the trains are seen on two tracks that are about to merge. Holmes states that there are no points left to switch. However, the coming together of the two track lines necessarily involves a switching point. And, in fact, that set of points is visible soon thereafter.
During the railroad pursuit as the two trains converge on adjacent tracks, the semaphore signal for the track on which the pasha's train runs is at "stop" (in the horizontal position).
When pointing out the items in Freud's study, Holmes indicates the menorah, which along with copies of the Hebrew Bible and the Talmud indicate Freud is Jewish. The problem is that it's a 9-candle menorah, which is only used during Hannukah. The rest of the year, a 7-candle menorah is used, and that's what would have been on Freud's desk. (And Holmes would have known this fact.) This being Freud's PRIVATE study, which he doesn't even allow the maid to clean, he could have a 9-candle menorah for any reason he chooses.
When Holmes shows Watson the vanilla, he points to a footprint & wheel rut in dry dirt which was obviously spread there for that purpose on top of the otherwise-clean but wet cobblestone road.
During the railroad pursuit right after the crew starts dismantling the carriage modern high-tension electrical transmission lines are seen atop a hill running parallel to the tracks.
Freud accuses Holmes of being "egocentric." However, the use of the term ego (Latin for "I") was not used by Freud until the 1920 and the psychological adjective "egocentricity" did not exist until after Freud established the concept of the ego, id and superego in his paper "The Ego and the Id" in 1923.
Watson, Holmes. Freud and the Orient Express line all refer to the train destination as Istanbul. However, Continental usage and railroad usage would have used the formal name "Constantinople" until the fall of the Ottoman Empire. Previously, although it had been referred to as Istanbul by locals, it was an informal name meaning "the city." It would never have been used thus by Holmes, Watson, Freud or the railroad.
Holmes tries to follow the man who debarks from the Pasha's carriage. He is rebuffed by guards and says "Saved from a profanation, Watson." However, Holmes can be seen speaking after that with no associated sound.
At about 1:00:13, as she describes the way she was abducted, Fräulein Devereaux - portrayed as an Austrian actress by Vanessa Redgrave - uses the nonstandard pronunciation of the word "landau," rhyming the last syllable with dough, rather than with Dow, which is the right pronunciation. This mistake is usually made by those who fail to recognize the word as German, but as an Austrian, whose mother tongue is German, Fräulein Devereaux should know how to pronounce it correctly.
On the train, Watson's narrative indicates he's aware of what Holmes is doing with the satchel. But at Freud's, he seems surprised by what he finds hidden in it. However, Watson never has the chance to see how much cocaine Holmes had hidden in the satchel until he searches it in Freud's home; his surprise comes from the great number of bottles that he finds in the secret compartment in the bottom of the bag.