An extensive Californian rail system that predates the 1856, 17-mile long Sacramento Valley Railroad, and connects with the Eastern Seaboard long before the 1869 First Transcontinental Railroad. The trains use modern rail couplers, which were invented in 1873.
Appearances of Confederate soldiers and discussion of "the Confederacy" as an organization within the United States, all before the secessions of 1861.
A map of the continental United States showing 48 states, instead of 31 including California delineates two states (Arizona and New Mexico) that did not achieve statehood until 1912. Several other states depicted on the map were also entered into the Union long after California. A flag at the signing ceremony at the end also appears with 48 stars.
The American agents who enlist Elena's help identify themselves as Pinkerton Agents. In 1850, the agency that Allan Pinkerton had just founded that year was called the North-Western Police Agency. Moreover, the Pinkertons did not serve the US government until Lincoln's administration.
Additional deviations include a quote from the Gettysburg Address, which would not be written until 1863. For some reason, the end credits list Abraham Lincoln himself as appearing at the California signing ceremony at the film's conclusion -- 10 years before he becomes President.
A reference to the country of Slovenia, which was not an independent nation until 1918.
Mexican-American Californios portrayed as full citizens, with voting rights, loyal to the Union. Most were treated as enemy aliens, having migrated from Sonora in Mexico to work the mines, and many were later expelled. Most had fought against the U.S. and white settlers.
Furthermore, a deleted scene on the film's DVD features a short discussion on a magic lantern presentation, first invented in 1870.