Other mistake: In the final scene when they are about to charge Fort Wagner, Mathew Broderick yells "forward march!" and takes his first step with his right foot when it should have been his left foot like the rest of the battalion.
Other mistake: In the scene where muskets are issued to the 54th Massachusetts, only Pvt. Jupiter Sharts is revealed to be a marksman worthy of training the other troops by virtue of having previously hunted squirrels. The camera then zooms to a closeup of Pvt. Sharts aiming down the barrel with the wrong eye closed.
Chosen answer: The shoes would have been a mix of the most common sizes, and the men would have gone through them to find the right size...swapping when necessary. Keep in mind many of them were barefoot, so even shoes of the wrong size would have been a blessing.