Accent Adaptation: Alexander the Great has an Irish accent as do many of his generals. The filmmakers did this on purpose, as Alexander was Macedonian, which at the time were considered much more rural and uncivilized than their Greek neighbors, and hypothesized that they sounded more like Celts, so they decided an Irish accent would be more realistic than anything else. On the other hand, Angelina Jolie affects an "exotic foreigner" accent (intended to be Albanian, which would fit her character's birthplace of Epirus, in modern-day Albania.)
Or, acording to the documentry about making of the film, Colin Farrell was unable to fully drop his Irish one, so instead everyone addopted it and then it went to the above described decision of Irish accent as Macedonian Greek.
Anachronic Order: The film starts with narration by Ptolemy, when he's at the end of his life. Then it keeps jumping on the events of Alexander conquest and early years. In shorter cuts it can be hard to follow with so many retrospections within retrospections.
Analogy Backfire: Alexander feels that Hephaistion is being less than optimistic over his plans.
Alexander: Did Patroclus stare at Achilles when they stood side by side at the siege of Troy?
Hephaistion: Patroclus died first.
This repeats itself, when in a flashback Aristotle is reminding everyone how selfish and egoistic Achilles was. Yet Alexander is styling himself as second Achilles for his whole life, perhaps too hard...
And Then What?: Hephaistion at one point asks Alexander what he would do once he conquered his way all the way to his much sought "Outer Ocean". Without missing a beat, Alexander turns to his boyfriend, and moral center, and answers: "I turn around and conquer the other half!"
Decapitated Army: Alexander plan for winning Gaugamela requires going right for Darius and slain him, which will destroy Persian ranks almost instantly.
Alexander: If I die, it's one Macedonian. But the Persians, they can't move without Darius command.
Deliberate Values Dissonance: Macedonians and other Greeks in general look down on all non-Greeks as hedonistic barbarians. When Alexander says that he looks forward to the day when Greeks and non-Greeks will mix and be treated as equals, his generals look at him as if he's insane. And there is of course heavy misogynistic theme on the Greek side, treating women as good for childbearing and slaves to passion, while only two man can create a true, perfect love.
Marital Rape License: Drunk Philip on Olympias. While young Alexander is watching. And it's alluded he doesn't need to be drunk for that.
Meaningful Background Event: Hephaistion's death scene: Alexander speaks with him, then goes to a window and makes a speech about his future conquests and their growing old together...meanwhile, in the background, very much out of focus, Hephaistion dies.
Mercy Kill: Glaucos, an Ilirian wounded by spear under Gaugamela is dying. The physician starts to unwrap a set for euthanasia while Alexander is comforting the soldier and then...
A Real Man Is a Killer: Phillip's father send him to battle and when he returned after slaying someone for the first time, he said "Now you know".
Rearing Horse: Alexander's horse rears as it faces an enemy War Elephant which is also rearing. Then he falls off from his horse.
Rousing Speech: At the Battle of Gaugamela, Alexander rides before his phalanx, pointing out individual soldiers and reminding them of their past heroic deeds. Then he addresses the army as a whole.
"Some of you, perhaps myself, will not live to see the sun set over these mountains today. But I tell you what every warrior has known since the beginning of time. Conquer your fear, and I promise you, you will conquer death!"
Royal Harem: One in Babylon. Which includes even androgynous boys with make up and longhair.
Royally Screwed Up: Alexander whole family - drunk rapist father, possesive and tretcherous mother, he himself lusting for everlasting glory of conqueror, then Roxane playing her own games... Not to mention his male lovers that he treats as part of his family.
Sex Is Evil: Or at least sex as a result of blind lust, which the film keeps on reminding quite often. Alexander surely wasn't the best student of Aristotle, given his deeds.
Spiked Wheels: Scythed chariots are shown charging into Macedonian phalanx during the beginning of Battle of Gaugamela scene.
Take That: Averted. While there are many digs toward Achilles, it was no-one intention to take them as an insult toward Troy.
At the Battle of the Hydaspes, Alexander throws his sword at King Poros in a futile attempt to kill him, only to miss.
In the Final Cut, during the Battle of Gaugamela, Antigonus (the one-eyed general) barely manages to protect himself with his shield from an arrow, and then conterattacks by tossing his sword at the Persian archer.
War Is Glorious: What everyone firmly believes. With time however, more and more Macedonians are tired with never-ending conquest and witnessing the hell of war for so many years. In the end, Alexander is forced to retreat, being the only one still lusting for more war.
War Is Hell: The scenes after the battles are not very subtle about this. So are the battles in extended cuts.
You No Take Candle: The Persians (and much of the Greeks/Macedonians) speak fairly and eloquently ("If only you were not a pale reflection of my mother's heart") whilst the Baktrian Roxane speaks in this manner: "Great man, Alexander? You I kill now." Potentially justified in showcasing that Roxane was not very fluent in the native language of the Greeks, while her father Oxyartes speaks perfectly fluent.