Audience-Alienating Premise: The theatrical cut gets this from some people. Since the cut focused on Stonewall Jackson as the primary—some might say sole—protagonist, it featured a primarily Southern POV. This made the Hollywood History elements of the script (like Jackson's slave cook being replaced with a freeman, skipping over major events like Antietam) stand out almost like propaganda. It's arguable all the scenes kept were necessary to maintain at least one full Character Arc, but when the film stops to feature an in-universe song and dance of "The Bonny Blue Flag" instead of addressing stuff like the Emancipation Proclamation...
Only two major black characters are featured in the story and both support the Confederacy, making it seem like most of the slaves supported the cause of the Confederacy (they did not).
There's a lot of whitewashing involving Jackson's views on slavery, making it seem like he opposed it, when most records said he supported it, or at the very least thought of it as a "necessary evil", though it's just as likely he thought of it as a right sanctioned by God like many of his peers.
Talk of Confederates freeing their slaves to join the Confederate army is suggested in the film, which takes place in the early to middle part of the war, when in reality the Confederacy only started taking the idea seriously in the final months of the war when they were truly desperate, and only with the proviso that armed black slaves would not be freed but would remain slaves. Even then many opposed the idea as madness.
At best, the film leans heavily into the narrative of the civil war as a "tragic misunderstanding." At worst, it's neo-Confederate propaganda. Among other issues raised: