It was raining on the day of the real chase (this is simply a deviation from the source material and a fact the filmmakers were likely aware of, which is why this is not listed as a goof).
Only thirteen pieces of equipment were actually used: two full-sized locomotives, one yard engine, three passenger cars, two iron box cars, and five wooden box cars that were built specifically to be destroyed in the film. The various pieces of equipment wore different numbers on different trains throughout the movie.
In the film there are 16 raiders. In reality there were actually 20 raiders that participated in the raid. There had initially been 24 raiders, but two joined Confederate forces after being stopped on their journey down to Marietta, as Andrews had instructed, and two more simply overslept and missed the train. These four were not depicted in the film as well as four others who participated.
The locomotive the plays The General in the film (Baltimore and Ohio #25 William Mason) was built around the same time as the General, and had been in service during the Civil War. This is also the same locomotive used as The Wanderer in Wild Wild West.
William Campbell is depicted in the film as a Union soldier. In real history, Campbell was the only civilian beside Andrews to participate in the raid; his character in the film is also quite different than his real life character.