* The death of Tyler: how come no one noticed it? It must have been quite loud all with that [[spoiler:giant mechanical bird fighting with him.]]
* Leaving the train in Vienna with the briefcase [[spoiler:full of gold]] and looking upset. If all he wanted to do in Jerusalem was studying a manuscript, and he ends the game [[spoiler:without the Firebird]] anyway, why couldn't he continue the journey? Yes, it would be brutal to force the player to revert all back to Vienna to see the canon ending, but there is no in-game explanation at all why he really needs to leave the train.
** Presumably, Schmidt or the Black Hand would have had something to say about keeping the gold if Cath hadn't hopped off the train and disappeared.
* How could Kronos catch up with them in Constantinople if he left at Vienna, and the Express didn't stop at and after Budapest at all?
** The only way that it's even remotely plausible is if he owns an aeroplane. Pretty damned unlikely, but nothing else fits.
*** In 1914 there were no aeroplanes which could transport hist luxury train car. Or maybe he owns or rents more than one in different stations.
*** Did he have his train car at the end of the game? I don't remember it being there. I only mentioned an aeroplane because it was the only way you could possibly outrun an express train in 1914. An expensive and unlikely solution - but Kronos is an expensive and unlikely sort of man.
* Where exactly did Anna hide between setting her free and fighting your way to the locomotive on the roof?
* Why is it the Austrian police who deal with them if they stop shortly before crossing the Serbian border? The military and part of the government of Austria-Hungary was common, but both the member states had their own police force. Even Anna gets this wrong, and not only is she of mixed Jewish-German-Hungarian ethnicity (as got together from some conversations) but she even [[spoiler:serves in the Austrian secret police]].
** By this point in time, the Black Hand had been effectively at war with the Habsburg Monarchy for at least a decade, and the Bosniak protectorate was in a state of siege while the rest of the border couldn't have been much more docile. The effective military occupation along the border coupled with the Austro-Hungarian chief of staff's obsession with destroying Serbia on *top* of the Hungarian-Slav problems in the Empire would probably have made it more convenient to station Austrians rather Hungarians. And as for [[spoiler: Anna, she could be faking it, or simplifying, assuming it is wrong.]]
* How did Vassili Alexandrovitch know about the exact nature of the Firebird? Tyler had it from the beginning, and when it ended up in his and his granddaughters bathroom, it was given by Anna for safekeeping.
** Chalk it up to supernatural hallucination/mind-reading with Robert. It's accepted that Robert uses some sort of hypnosis at several points in the game to 'calm' people down. And the tea he's giving him is a strong poison with psychedelic and hallucinogenic properties.
* Why do August Schmidt and Anna speak English between each other most of the time, even if no one else is around? It's not TranslationConvention, as they even compliment each other about their English, and all other characters speak their respective languages between each other.
** It used to be a sign of prestige and upper-class sophistication to speak a language other than your native one. Presumably, Schmidt and Wolff are just trying to show off. (Alternatively, they're trying to keep their English skills sharp because they're the only German speakers besides Cath on the train and they don't speak French.) Another question is why various texts written or held by characters (Schmidt's letter, Anna's letter, and Tatiana's note) are written in English.
*** Possibly as a form of encryption. The letters to Anna and from Schmidt would probably pass through messengers, and if those messengers can't read English, then they can't betray the sender. As for Tatiana's note, possibly she didn't want her Grandfather to be able to read it in case he saw it.
* Why do Anna, George, and the conductor watch over your shoulder as you defuse the bomb when they should be evacuating the train? The man who planted the bomb is no longer a threat by that point, so they needn't worry about the evacuation causing further trouble.
** They likely don't want to report the incident. George's immediate conversation with the conductor after Alexei dies is about how George has influence with the Austrians and will be able to smooth things over and keep it from becoming a blight on the service record of the Orient Express. (And enable the workers to all keep their jobs, likely.)