During the robbery of the payroll train, up the track in the direction of the train's travel, there are modern CTC block signals of the Southern Pacific Railroad which were installed in the 1930s (beyond the siding switch). Centralized Traffic Control for railroads did not exist in 1865, nor did the heavier rail on the right of way shown in the film (at least 100 pounds).
When the brothers try to coerce the other former soldiers into turning in the money, they disarm the three. As the camera angles switch one guy has his jacket covering his holster, then it is exposed with the gun still still in it, then switches back to being concealed.
The Civil War did not end all at once on April 9, 1865. The surrender and ceasefire on that date applied only to General Robert E. Lee's Confederate Army of Northern Virginia and the Virginia theater of operations. The other large Confederate army, General Joseph E. Johnston's Army of Tennessee, did not surrender until April 26, and smaller elements of Confederates throughout the country (which were incommunicado, such as the cavalry brigade that the Reno brothers belonged to) continued to fight until the news of Johnston's surrender reached them through the slow communications of the day, well into the summer of 1865. (While that fact would not necessarily prevent the charges of robbery leveled by the Federal government against the the Reno brothers, it would make a compelling legal defense for them.)
The goof item below may give away important plot points.
When the Reno brothers are arrested at the future school grounds, the Federals mention that they had robbed the train "on April 10th, eight weeks ago", dating that scene in early June. Yet Clint is killed the next day and, in the closing scene the date of death on his headstone reads "April 25, 1865".