Continuity mistake: When Alexander builds an altar for Titans to mark the furthest point he has reached, both him and Hephaestion are reasonably recovered from severe wounds they suffered during the battle of Hydaspes, which was the last battle mentioned. However, we can see scratches and minor injuries on many characters' faces that appear very fresh and would have disappeared without a trace in the time it took for the deeper wounds to heal.
Continuity mistake: Towards the beginning of the movie, young Alexander is receiving a wrestling lesson and his hair is extremely blonde. A short time later, young Alexander is outside with his teacher and fellow students and his hair is more brownish-blonde. (00:05:45)
Continuity mistake: During the battle of Gaugamela when Macedonian and Persian cavalry are riding in parallel (with Macedonian infantry hiding behind the cavalry) Alexander gives an order for the cavalry to turn left and the infantry to go forward. In detailed shots from the ground we can see the horses slowing down and turning. But in the wide shot from above we can see the infantry turning left instead to emerge from between the horses and the cavalry continue to ride straight in the original direction.
Continuity mistake: In the scene were Queen Olympias is walking towards Alexander with a snake around her arm, there is a two second clip at Alexander and then Olympias is seen again but not holding the snake anymore. (00:09:30)
Continuity mistake: The scar on Old Ptolemy's forehead switches sides halfway through his first scene.
