Esoteric Happy Ending: Hooray, Johnnie's won back his lady love and gotten into the army! Sounds very happy, but then remember how the civil war ends for the South. Johnnie's going to be lucky not to get himself killed in the following battles, and even if he survives he and Annabelle aren't going to have a very fun future ahead of them...
I Am Not Shazam: The central character's name is not "The General", it's Johnnie Gray. "The General" is the name of his locomotive.
Memetic Mutation: Picturing Keaton as Johnnie Gray sitting on the moving of the titular locomotive has become pretty popular.
Values Dissonance: It can feel pretty odd being asked to root for the Confederate army over the Union, plus the way that Annabelle becomes The Load on the return trip. The film is based on a real-life incident during the war, and Buster Keaton stated that he felt that William Allen Fuller, the real-life conductor Confederate campaign, chasing the runaway train by foot, handcart and other means, came off as the Villainous Underdog. Keaton felt that changing the story to make Fuller a Union man would be Politically Correct History (though at the time the film was madenote the height of Lost Cause historiography, it was very much the norm).
Vindicated by History: A flop upon release, it is now considered a classic and one of the best films of the silent era.